Table S1 is iPSN differentiation protocols
multiqc_stat_paths = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir) %>% mutate(multiqc_stat_paths = paste0(database_dir,"/nfcore/multiqc/star_salmon/multiqc_data/multiqc_general_stats.txt"),
# multiqc_stat_paths = gsub("/camp/lab/luscomben/home/users/ziffo|/camp/project","/Volumes/lab-luscomben/home/users/ziffo",multiqc_stat_paths)
) %>% pull(multiqc_stat_paths)
multiqc_stats.tsv = multiqc_stat_paths %>% map(read_tsv, show_col_types = FALSE)
names(multiqc_stats.tsv) = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir,.keep_all=TRUE) %>% pull(dataset)
multiqc_data <- map_dfr(multiqc_stats.tsv, bind_rows, .id = "dataset") %>% clean_names() %>% drop_na(samtools_mqc_generalstats_samtools_flagstat_total) %>% filter(sample %in% ipsc_mn_als_datasets_with_lee.metadata$sample) %>%
mutate(dataset = case_when(dataset == "neurolincs0" & grepl("^0007",sample) ~ "neurolincs_diMN", dataset == "neurolincs0" & grepl("^A-042",sample) ~ "neurolincs_iMN", dataset == "answerals" ~ "AnswerALS", dataset %in% c("dafinca.c9orf72","dafinca.tardbp") ~ "dafinca", TRUE ~ dataset)) %>%
select(dataset, sample, raw_total_sequences = samtools_mqc_generalstats_samtools_raw_total_sequences, flagstat_total = samtools_mqc_generalstats_samtools_flagstat_total, mapped_passed = samtools_mqc_generalstats_samtools_mapped_passed, reads_mapped = samtools_mqc_generalstats_samtools_reads_mapped, reads_mapped_percent = samtools_mqc_generalstats_samtools_reads_mapped_percent, reads_aligned = quali_map_mqc_generalstats_qualimap_reads_aligned, r_rna_percent = biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna, bias_5_3 = quali_map_mqc_generalstats_qualimap_5_3_bias, proper_pairs_percent = r_se_qc_mqc_generalstats_rseqc_proper_pairs_percent, reads_assigned_percent = feature_counts_mqc_generalstats_featurecounts_percent_assigned, reads_assigned = feature_counts_mqc_generalstats_featurecounts_assigned, percent_duplication = picard_mqc_generalstats_picard_percent_duplication, error_rate = samtools_mqc_generalstats_samtools_error_rate, non_primary_alignments = samtools_mqc_generalstats_samtools_non_primary_alignments, reads_properly_paired_percent = samtools_mqc_generalstats_samtools_reads_properly_paired_percent, percent_mapped = salmon_mqc_generalstats_salmon_percent_mapped, num_mapped = salmon_mqc_generalstats_salmon_num_mapped, uniquely_mapped_percent = star_mqc_generalstats_star_uniquely_mapped_percent, uniquely_mapped = star_mqc_generalstats_star_uniquely_mapped, percent_trimmed =cutadapt_mqc_generalstats_cutadapt_percent_trimmed, total_sequences = fast_qc_mqc_generalstats_fastqc_total_sequences, raw_percent_gc = fast_qc_raw_mqc_generalstats_fastqc_raw_percent_gc, raw_avg_sequence_length = fast_qc_raw_mqc_generalstats_fastqc_raw_avg_sequence_length, trimmed_percent_duplicates = fast_qc_trimmed_mqc_generalstats_fastqc_trimmed_percent_duplicates, trimmed_percent_gc = fast_qc_trimmed_mqc_generalstats_fastqc_trimmed_percent_gc)
kbl(multiqc_data) %>% kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), fixed_thead = T) %>% scroll_box(width = "100%", height = "500px")| dataset | sample | raw_total_sequences | flagstat_total | mapped_passed | reads_mapped | reads_mapped_percent | reads_aligned | r_rna_percent | bias_5_3 | proper_pairs_percent | reads_assigned_percent | reads_assigned | percent_duplication | error_rate | non_primary_alignments | reads_properly_paired_percent | percent_mapped | num_mapped | uniquely_mapped_percent | uniquely_mapped | percent_trimmed | total_sequences | raw_percent_gc | raw_avg_sequence_length | trimmed_percent_duplicates | trimmed_percent_gc |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AnswerALS | CASE_NEUAA599TMX | 90172968 | 110049375 | 110049375 | 90172968 | 100 | 45083935 | 0.0000341 | 0.99 | 67.98135 | 42.58702 | 23434669 | 0.143612 | 0.0024970 | 19876407 | 99.99435 | 100 | 24209931 | 92.84 | 42383420 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAB000NKC | 89923754 | 126498124 | 126498124 | 89923754 | 100 | 44958805 | 0.0005546 | 0.98 | 53.83124 | 44.75184 | 28306923 | 0.209232 | 0.0027416 | 36574370 | 99.99317 | 100 | 29638747 | 89.01 | 40901591 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAE228FF6 | 130825845 | 271586963 | 271586963 | 130825845 | 100 | 65399474 | 0.0007375 | 0.98 | 22.06248 | 22.76193 | 30915467 | 0.514356 | 0.0017731 | 140761118 | 99.97944 | 100 | 33394237 | 79.24 | 53277634 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAE993EPR | 125072312 | 165724188 | 165724188 | 125072312 | 100 | 62531785 | 0.0003629 | 1.01 | 54.17946 | 44.55271 | 36920158 | 0.254615 | 0.0020875 | 40651876 | 99.99301 | 100 | 39957256 | 88.95 | 56894281 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAF553MJ3 | 111693376 | 150525878 | 150525878 | 111693376 | 100 | 55843369 | 0.0007157 | 0.96 | 59.10802 | 33.41668 | 25151814 | 0.173674 | 0.0027145 | 38832502 | 99.99406 | 100 | 26254962 | 89.88 | 51139673 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAG241NUD | 128635564 | 176979996 | 176979996 | 128635564 | 100 | 64313593 | 0.0002679 | 1.00 | 48.16291 | 37.53702 | 33218721 | 0.312094 | 0.0020796 | 48344432 | 99.99349 | 100 | 35528664 | 88.92 | 58281646 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAG603XLK | 49130010 | 65504049 | 65504049 | 49130010 | 100 | 24563226 | 0.0000682 | 0.97 | 60.69713 | 40.28262 | 13194300 | 0.158176 | 0.0027302 | 16374039 | 99.99276 | 100 | 13971295 | 90.56 | 22629235 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAG766ULB | 126929964 | 183940593 | 183940593 | 126929964 | 100 | 63460674 | 0.0001364 | 0.97 | 44.39181 | 36.66220 | 33721322 | 0.327647 | 0.0019348 | 57010629 | 99.99321 | 100 | 38009904 | 86.00 | 55851641 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAL076FCE | 131833174 | 167516336 | 167516336 | 131833174 | 100 | 65912690 | 0.0001157 | 1.00 | 51.01627 | 46.44480 | 38903923 | 0.328565 | 0.0020416 | 35683162 | 99.99409 | 100 | 41680265 | 90.36 | 60722395 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAM655HF7 | 87433717 | 136427989 | 136427989 | 87433717 | 100 | 43714307 | 0.0007112 | 0.97 | 49.04198 | 35.24584 | 24043842 | 0.198245 | 0.0026647 | 48994272 | 99.99416 | 100 | 25533781 | 87.06 | 38824703 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAP285GGU | 105486258 | 156711695 | 156711695 | 105486258 | 100 | 52739534 | 0.0001533 | 0.99 | 43.73658 | 32.45820 | 25434619 | 0.320706 | 0.0021994 | 51225437 | 99.99318 | 100 | 27807432 | 86.72 | 46727085 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAT234RK6 | 120938977 | 151644990 | 151644990 | 120938977 | 100 | 60463545 | 0.0000474 | 1.01 | 55.15200 | 41.70809 | 31627358 | 0.283175 | 0.0020793 | 30706013 | 99.99017 | 100 | 34225046 | 89.90 | 55453618 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAW157NMJ | 114977089 | 145878754 | 145878754 | 114977089 | 100 | 57485309 | 0.0000300 | 0.98 | 62.68947 | 45.63163 | 33285218 | 0.176876 | 0.0026261 | 30901665 | 99.99437 | 100 | 34142140 | 92.00 | 53691857 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAW717TN6 | 126834297 | 159575177 | 159575177 | 126834297 | 100 | 63405958 | 0.0000835 | 1.00 | 58.45321 | 34.49994 | 27532068 | 0.239585 | 0.0019821 | 32740880 | 99.98235 | 100 | 28895482 | 90.26 | 58851386 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAX665ZHY | 139537273 | 231443631 | 231443631 | 139537273 | 100 | 69763285 | 0.0002681 | 0.98 | 39.84617 | 29.65286 | 34317241 | 0.309280 | 0.0019313 | 91906358 | 99.99233 | 100 | 38214892 | 84.78 | 60401717 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAY067UTB | 153856323 | 214267305 | 214267305 | 153856323 | 100 | 76923947 | 0.0005954 | 1.02 | 46.70964 | 36.05257 | 38626623 | 0.324427 | 0.0020446 | 60410982 | 99.99452 | 100 | 41699625 | 88.96 | 69716387 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUAZ394JEZ | 134436051 | 178480252 | 178480252 | 134436051 | 100 | 67210701 | 0.0001388 | 1.00 | 48.50850 | 37.12241 | 33133119 | 0.328293 | 0.0022132 | 44044201 | 99.98910 | 100 | 37250812 | 86.85 | 60348215 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUBA169GXD | 123489072 | 183039179 | 183039179 | 123489072 | 100 | 61738330 | 0.0002351 | 1.01 | 47.16187 | 38.10750 | 34879845 | 0.270775 | 0.0019934 | 59550107 | 99.98995 | 100 | 37301727 | 85.89 | 54952243 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUBC901KL3 | 128790984 | 158512044 | 158512044 | 128790984 | 100 | 64386445 | 0.0001962 | 0.99 | 58.53930 | 45.65992 | 36193674 | 0.253956 | 0.0019522 | 29721060 | 99.98595 | 100 | 37879352 | 91.83 | 60115760 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUBC998WWB | 135317031 | 201372187 | 201372187 | 135317031 | 100 | 67654064 | 0.0005399 | 0.97 | 46.27861 | 33.47649 | 33708237 | 0.280293 | 0.0020378 | 66055156 | 99.99342 | 100 | 35826821 | 87.60 | 60600596 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUBD218YR3 | 94340954 | 144759706 | 144759706 | 94340954 | 100 | 47167578 | 0.0000192 | 0.98 | 48.05228 | 43.19240 | 31264298 | 0.227102 | 0.0027411 | 50418752 | 99.99385 | 100 | 34033859 | 87.16 | 41925594 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUBD288RXQ | 116501755 | 146458489 | 146458489 | 116501755 | 100 | 58246918 | 0.0002148 | 0.94 | 60.91542 | 28.60820 | 20951015 | 0.209542 | 0.0021196 | 29956734 | 99.99320 | 100 | 21670764 | 91.97 | 54377155 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUBK117YXL | 124612330 | 176723226 | 176723226 | 124612330 | 100 | 62302088 | 0.0011893 | 1.00 | 50.17024 | 34.82647 | 30775311 | 0.258965 | 0.0021462 | 52110896 | 99.99346 | 100 | 32249185 | 88.26 | 56369904 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUBM949LA5 | 123889216 | 181640803 | 181640803 | 123889216 | 100 | 61938822 | 0.0003055 | 1.00 | 45.47430 | 36.03590 | 32731139 | 0.303790 | 0.0020690 | 57751587 | 99.99066 | 100 | 35619732 | 87.21 | 55164621 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUBN979ZZ5 | 121537754 | 158678819 | 158678819 | 121537754 | 100 | 60763327 | 0.0000682 | 1.01 | 54.39141 | 44.35331 | 35193014 | 0.260889 | 0.0018488 | 37141065 | 99.99087 | 100 | 38577212 | 89.17 | 55260530 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUBT273FH3 | 110747555 | 139595936 | 139595936 | 110747555 | 100 | 55368342 | 0.0002129 | 1.01 | 51.51089 | 49.11158 | 34282757 | 0.326915 | 0.0019341 | 28848381 | 99.99018 | 100 | 38296907 | 89.49 | 50443790 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUBW008RJ5 | 148445384 | 191169979 | 191169979 | 148445384 | 100 | 74215056 | 0.0000695 | 1.00 | 53.75423 | 42.16076 | 40303598 | 0.281581 | 0.0020311 | 42724595 | 99.98971 | 100 | 43213983 | 90.70 | 68428153 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUBY734PFR | 89534532 | 117260923 | 117260923 | 89534532 | 100 | 44764400 | 0.0002683 | 0.96 | 61.13324 | 42.59420 | 24974733 | 0.168385 | 0.0027772 | 27726391 | 99.99360 | 100 | 26194066 | 90.53 | 41347426 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCB613CA9 | 120314012 | 157070980 | 157070980 | 120314012 | 100 | 60153084 | 0.0001226 | 0.98 | 55.67521 | 38.41598 | 30172303 | 0.247442 | 0.0019572 | 36756968 | 99.99348 | 100 | 32529148 | 89.89 | 55041136 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCD502BFU | 122416921 | 163718351 | 163718351 | 122416921 | 100 | 61200013 | 0.0002703 | 0.98 | 52.61787 | 44.28361 | 36255523 | 0.268173 | 0.0020632 | 41301430 | 99.98620 | 100 | 37130970 | 90.10 | 56342440 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCE965ZGK | 99739464 | 146713178 | 146713178 | 99739464 | 100 | 49866419 | 0.0000423 | 0.97 | 51.30799 | 41.90401 | 30741292 | 0.211673 | 0.0026514 | 46973714 | 99.99336 | 100 | 32466869 | 88.12 | 44747465 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCF538BRM | 124776812 | 147487594 | 147487594 | 124776812 | 100 | 62382563 | 0.0000829 | 0.98 | 64.21820 | 40.91160 | 30172840 | 0.218006 | 0.0021087 | 22710782 | 99.99063 | 100 | 31309221 | 92.23 | 58712724 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCG511MJ6 | 141403477 | 188997248 | 188997248 | 141403477 | 100 | 70694493 | 0.0001681 | 0.97 | 50.33612 | 39.01470 | 36872585 | 0.301172 | 0.0022295 | 47593771 | 99.98975 | 100 | 39203261 | 88.35 | 64401376 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCN596RR3 | 107638838 | 136547448 | 136547448 | 107638838 | 100 | 53815848 | 0.0002137 | 0.97 | 63.39855 | 39.05644 | 26667044 | 0.168394 | 0.0027305 | 28908610 | 99.99336 | 100 | 28293153 | 91.27 | 49945306 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCP218XVV | 133693665 | 206523773 | 206523773 | 133693665 | 100 | 66837184 | 0.0005851 | 0.97 | 43.34389 | 36.40578 | 37599113 | 0.298408 | 0.0020207 | 72830108 | 99.98557 | 100 | 39426915 | 85.76 | 59265499 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCT022VTK | 139555913 | 173337477 | 173337477 | 139555913 | 100 | 69771316 | 0.0000122 | 0.96 | 56.24646 | 47.25522 | 40959489 | 0.277179 | 0.0020943 | 33781564 | 99.99048 | 100 | 42662232 | 91.68 | 64970108 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCT842RJV | 132288250 | 170017088 | 170017088 | 132288250 | 100 | 66141468 | 0.0000451 | 0.98 | 48.80887 | 49.59928 | 42165473 | 0.348855 | 0.0018535 | 37728838 | 99.99598 | 100 | 47530437 | 89.52 | 60131099 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCU076ADN | 138846225 | 192907404 | 192907404 | 138846225 | 100 | 69417377 | 0.0004188 | 0.99 | 47.60645 | 44.06356 | 42504669 | 0.310876 | 0.0018324 | 54061179 | 99.99174 | 100 | 45038105 | 88.31 | 62770985 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCU245GBQ | 89412399 | 120947846 | 120947846 | 89412399 | 100 | 44703436 | 0.0000910 | 0.96 | 57.40010 | 45.43816 | 27479901 | 0.193442 | 0.0027497 | 31535447 | 99.99382 | 100 | 29510050 | 89.99 | 40911080 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUCV578DFJ | 111373277 | 166478871 | 166478871 | 111373277 | 100 | 55679121 | 0.0002071 | 0.98 | 41.35444 | 32.47711 | 27037653 | 0.353243 | 0.0021349 | 55105594 | 99.98650 | 100 | 30515895 | 84.67 | 48770148 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUDD018KAH | 88045557 | 122378672 | 122378672 | 88045557 | 100 | 44020125 | 0.0003412 | 0.99 | 55.66305 | 44.06664 | 26965653 | 0.196328 | 0.0026667 | 34333115 | 99.99397 | 100 | 28593991 | 89.49 | 40078342 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUDE902GCT | 99937040 | 135441084 | 135441084 | 99937040 | 100 | 49965149 | 0.0002740 | 0.99 | 57.04999 | 46.88175 | 31750639 | 0.195966 | 0.0027189 | 35504044 | 99.99325 | 100 | 33903856 | 89.67 | 45708501 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUDG000ZG5 | 100589599 | 165876997 | 165876997 | 100589599 | 100 | 50291866 | 0.0006254 | 0.99 | 46.05712 | 27.37350 | 22704273 | 0.205570 | 0.0027085 | 65287398 | 99.99417 | 100 | 24022760 | 86.49 | 44142529 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUDG272XWC | 119792730 | 177927759 | 177927759 | 119792730 | 100 | 59890533 | 0.0006492 | 1.00 | 44.32943 | 35.83447 | 31883115 | 0.312701 | 0.0019648 | 58135029 | 99.99026 | 100 | 36165777 | 85.26 | 52442197 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUDH063DEA | 105591880 | 147314413 | 147314413 | 105591880 | 100 | 52792270 | 0.0001292 | 0.97 | 43.49162 | 44.14237 | 32517163 | 0.368034 | 0.0018514 | 41722533 | 99.99305 | 100 | 34872581 | 88.71 | 47660863 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUDM949BAR | 128202048 | 287681995 | 287681995 | 128202048 | 100 | 64098089 | 0.0001448 | 1.03 | 25.96516 | 19.68364 | 28314124 | 0.380233 | 0.0022874 | 159479947 | 99.99542 | 100 | 32796971 | 77.47 | 51012285 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUDP155HFH | 139462948 | 169095371 | 169095371 | 139462948 | 100 | 69727255 | 0.0001219 | 0.98 | 60.02936 | 46.56030 | 39368193 | 0.248814 | 0.0018828 | 29632423 | 99.99395 | 100 | 42287242 | 91.81 | 64911812 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUDT709YHN | 98823893 | 124576566 | 124576566 | 98823893 | 100 | 49409281 | 0.0001435 | 1.01 | 62.71525 | 43.64291 | 27185855 | 0.182869 | 0.0025115 | 25752673 | 99.99461 | 100 | 29035636 | 91.79 | 45965043 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUDY534KGP | 141589390 | 224129099 | 224129099 | 141589390 | 100 | 70790345 | 0.0005739 | 0.98 | 38.78086 | 31.40492 | 35195960 | 0.357183 | 0.0021470 | 82539709 | 99.99386 | 100 | 38758487 | 85.07 | 61667082 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUDZ473EGM | 154600775 | 199257878 | 199257878 | 154600775 | 100 | 77292269 | 0.0001501 | 0.98 | 54.35758 | 42.13185 | 41979848 | 0.273593 | 0.0020343 | 44657103 | 99.98950 | 100 | 45298101 | 89.96 | 70716346 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUEB422WW0 | 130660148 | 179922487 | 179922487 | 130660148 | 100 | 65326217 | 0.0002187 | 0.97 | 55.14692 | 45.24011 | 40700856 | 0.211997 | 0.0026283 | 49262339 | 99.99410 | 100 | 42774565 | 89.96 | 59731414 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUEC400NYR | 125412392 | 189213757 | 189213757 | 125412392 | 100 | 62698769 | 0.0000618 | 0.98 | 46.63567 | 32.48969 | 30741078 | 0.263394 | 0.0020064 | 63801365 | 99.98816 | 100 | 33532156 | 85.61 | 55448738 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUEK191WYC | 106345287 | 143788123 | 143788123 | 106345287 | 100 | 53169399 | 0.0003434 | 0.99 | 56.49555 | 44.95985 | 32325352 | 0.206117 | 0.0025269 | 37442836 | 99.99390 | 100 | 34889663 | 89.84 | 48514495 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUEM029XXZ | 93028028 | 116184964 | 116184964 | 93028028 | 100 | 46511187 | 0.0000987 | 0.98 | 64.36809 | 45.35590 | 26350014 | 0.168057 | 0.0025941 | 23156936 | 99.99392 | 100 | 27645965 | 91.84 | 43343592 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUEM720BUU | 86141784 | 131324319 | 131324319 | 86141784 | 100 | 43068135 | 0.0002889 | 0.97 | 46.29251 | 40.06190 | 26307070 | 0.259890 | 0.0029109 | 45182535 | 99.99360 | 100 | 29496177 | 86.04 | 37987180 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUEN017PCJ | 130567564 | 222562143 | 222562143 | 130567564 | 100 | 65279499 | 0.0005546 | 0.98 | 38.82526 | 29.48605 | 32814502 | 0.304728 | 0.0020111 | 91994579 | 99.99344 | 100 | 35304279 | 84.03 | 56203623 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUEN476CLW | 93313194 | 124980814 | 124980814 | 93313194 | 100 | 46653389 | 0.0002496 | 0.98 | 58.79835 | 45.51679 | 28445515 | 0.179232 | 0.0028058 | 31667620 | 99.99312 | 100 | 30075286 | 90.15 | 42774630 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUET072VDG | 141595402 | 188283258 | 188283258 | 141595402 | 100 | 70794354 | 0.0001037 | 1.00 | 48.77956 | 45.04774 | 42410775 | 0.326791 | 0.0020269 | 46687856 | 99.99527 | 100 | 46245461 | 89.47 | 64389846 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUEU318NY2 | 134884750 | 201782160 | 201782160 | 134884750 | 100 | 67439023 | 0.0003835 | 1.01 | 43.29325 | 34.36975 | 34677910 | 0.323295 | 0.0020267 | 66897410 | 99.99503 | 100 | 38364153 | 86.00 | 59255159 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUEU558MNK | 100521886 | 138251806 | 138251806 | 100521886 | 100 | 50257610 | 0.0002044 | 1.00 | 58.04566 | 40.34897 | 27893309 | 0.172240 | 0.0027409 | 37729920 | 99.99337 | 100 | 28934684 | 90.09 | 46268251 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUEY478NZP | 123856364 | 161856132 | 161856132 | 123856364 | 100 | 61925206 | 0.0001457 | 1.01 | 49.49657 | 48.32963 | 39114279 | 0.326938 | 0.0018693 | 37999768 | 99.99519 | 100 | 43542860 | 89.22 | 56068266 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUFB989DT1 | 97111909 | 119493426 | 119493426 | 97111909 | 100 | 48553082 | 0.0003310 | 0.98 | 65.46732 | 42.98284 | 25682366 | 0.167866 | 0.0025665 | 22381517 | 99.99408 | 100 | 27242345 | 92.20 | 45373156 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUFH122WN7 | 139072399 | 163898369 | 163898369 | 139072399 | 100 | 69531586 | 0.0000398 | 0.98 | 64.35023 | 36.80086 | 30160047 | 0.219188 | 0.0019883 | 24825970 | 99.99337 | 100 | 30026682 | 93.49 | 65888103 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUFH461AAN | 136572099 | 178778483 | 178778483 | 136572099 | 100 | 68282467 | 0.0002066 | 0.99 | 51.64257 | 38.98675 | 34851914 | 0.298697 | 0.0023940 | 42206384 | 99.99475 | 100 | 37275738 | 89.44 | 62183816 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUFU395MJD | 106078669 | 150927010 | 150927010 | 106078669 | 100 | 53033252 | 0.0003335 | 0.97 | 46.37928 | 36.14942 | 27282828 | 0.311878 | 0.0020394 | 44848341 | 99.98853 | 100 | 30319443 | 87.29 | 47215106 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUFV237VCZ | 116591551 | 142251705 | 142251705 | 116591551 | 100 | 58289922 | 0.0000931 | 0.98 | 60.75871 | 40.78029 | 29008424 | 0.233622 | 0.0020568 | 25660154 | 99.98996 | 100 | 29905603 | 91.78 | 54588104 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUFX386KMB | 136454440 | 179241166 | 179241166 | 136454440 | 100 | 68222312 | 0.0000788 | 0.98 | 52.12221 | 43.88143 | 39329613 | 0.289722 | 0.0020814 | 42786726 | 99.99281 | 100 | 42433048 | 89.66 | 62381253 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUFY342UNG | 118184565 | 150571375 | 150571375 | 118184565 | 100 | 59087606 | 0.0001005 | 0.99 | 58.35599 | 38.33532 | 28863430 | 0.230310 | 0.0018508 | 32386810 | 99.99209 | 100 | 31272225 | 89.91 | 54126474 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUGD965XVD | 136583771 | 169896591 | 169896591 | 136583771 | 100 | 68287240 | 0.0002035 | 1.02 | 59.11176 | 45.68885 | 38814619 | 0.241102 | 0.0019518 | 33312820 | 99.99320 | 100 | 40989816 | 91.63 | 63555884 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUGE540TC4 | 75422741 | 95453478 | 95453478 | 75422741 | 100 | 37708985 | 0.0004707 | 1.00 | 64.92686 | 41.39750 | 19758910 | 0.150972 | 0.0026750 | 20030737 | 99.99367 | 100 | 20586436 | 91.90 | 35209660 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUGH995TFK | 133045485 | 181931315 | 181931315 | 133045485 | 100 | 66515692 | 0.0000703 | 0.97 | 45.06227 | 42.23993 | 38428248 | 0.358487 | 0.0017872 | 48885830 | 99.98940 | 100 | 42594183 | 87.29 | 59472955 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUGJ081HKR | 92827431 | 129592427 | 129592427 | 92827431 | 100 | 46411223 | 0.0002330 | 0.99 | 55.89339 | 40.40376 | 26181432 | 0.187137 | 0.0026103 | 36764996 | 99.99463 | 100 | 28115190 | 89.63 | 42254938 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUGL543NJ1 | 122243099 | 155846140 | 155846140 | 122243099 | 100 | 61116951 | 0.0001317 | 1.01 | 57.60356 | 38.98401 | 30380271 | 0.239767 | 0.0019417 | 33603041 | 99.99248 | 100 | 32357464 | 90.50 | 56279458 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUGP781PDU | 99089507 | 123260123 | 123260123 | 99089507 | 100 | 49542192 | 0.0000507 | 0.97 | 63.37958 | 48.03670 | 29606571 | 0.184248 | 0.0024666 | 24170616 | 99.99483 | 100 | 31353374 | 91.95 | 46168118 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUGR121TFD | 141091397 | 199599129 | 199599129 | 141091397 | 100 | 70536352 | 0.0001659 | 0.98 | 49.49694 | 36.83002 | 36761388 | 0.270829 | 0.0021551 | 58507732 | 99.98675 | 100 | 38723194 | 86.77 | 63614335 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUGR539MVT | 134594246 | 172095822 | 172095822 | 134594246 | 100 | 67286121 | 0.0001557 | 1.00 | 52.87871 | 45.50994 | 39167316 | 0.300302 | 0.0021235 | 37501576 | 99.98365 | 100 | 42249514 | 89.43 | 61521240 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUGW326BRV | 86942871 | 119710782 | 119710782 | 86942871 | 100 | 43469101 | 0.0002033 | 0.98 | 56.16165 | 39.44430 | 23610810 | 0.195022 | 0.0026380 | 32767911 | 99.99463 | 100 | 25361092 | 89.90 | 39656424 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUGW340YEB | 136692973 | 183476162 | 183476162 | 136692973 | 100 | 68340429 | 0.0000880 | 1.00 | 51.60555 | 38.39680 | 35227745 | 0.279955 | 0.0019997 | 46783189 | 99.99114 | 100 | 38284910 | 89.09 | 62053078 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHB491NGF | 145522197 | 202221470 | 202221470 | 145522197 | 100 | 72753784 | 0.0002094 | 0.96 | 50.41580 | 31.63419 | 31988783 | 0.272387 | 0.0020442 | 56699273 | 99.98995 | 100 | 32812161 | 89.01 | 66227888 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHG644RYB | 138979998 | 201813224 | 201813224 | 138979998 | 100 | 69482706 | 0.0001692 | 1.01 | 45.87918 | 38.66221 | 39017272 | 0.304173 | 0.0018454 | 62833226 | 99.98950 | 100 | 43918370 | 85.05 | 60646533 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHG791RV5 | 119400996 | 160767092 | 160767092 | 119400996 | 100 | 59697027 | 0.0000261 | 0.99 | 56.18658 | 42.85333 | 34448962 | 0.214817 | 0.0025435 | 41366096 | 99.99419 | 100 | 36903652 | 90.01 | 54523059 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHK991AVP | 150076387 | 203632648 | 203632648 | 150076387 | 100 | 75035119 | 0.0003553 | 0.99 | 45.16991 | 45.32742 | 46152868 | 0.363986 | 0.0018715 | 53556261 | 99.99590 | 100 | 51372601 | 88.06 | 67327991 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHL999WWT | 120914707 | 152068342 | 152068342 | 120914707 | 100 | 60453335 | 0.0002409 | 0.99 | 58.29780 | 42.58072 | 32378390 | 0.242050 | 0.0020147 | 31153635 | 99.99335 | 100 | 34087609 | 91.26 | 56126841 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHM532NDD | 132018194 | 177570876 | 177570876 | 132018194 | 100 | 66004538 | 0.0005658 | 0.99 | 53.15327 | 33.04001 | 29336787 | 0.257687 | 0.0020835 | 45552682 | 99.99309 | 100 | 31431334 | 89.17 | 60004909 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHT569HT1 | 135726690 | 175838065 | 175838065 | 135726690 | 100 | 67856787 | 0.0001545 | 0.98 | 53.70584 | 36.81147 | 32367583 | 0.278507 | 0.0021176 | 40111375 | 99.99034 | 100 | 34696832 | 89.43 | 62178209 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHV216EHA | 137327199 | 187736616 | 187736616 | 137327199 | 100 | 68658564 | 0.0011124 | 0.96 | 51.74819 | 31.40976 | 29486017 | 0.266897 | 0.0020767 | 50409417 | 99.99267 | 100 | 31516294 | 88.75 | 62223182 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHW530WD8 | 142706149 | 186097772 | 186097772 | 142706149 | 100 | 71346968 | 0.0001573 | 0.98 | 54.96032 | 43.72086 | 40685469 | 0.257348 | 0.0020625 | 43391623 | 99.99144 | 100 | 42259547 | 90.23 | 65688979 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHW590KBH | 87895366 | 120494665 | 120494665 | 87895366 | 100 | 43945090 | 0.0001100 | 0.98 | 57.59010 | 39.21984 | 23630275 | 0.178782 | 0.0025832 | 32599299 | 99.99410 | 100 | 25159813 | 89.88 | 40130196 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHY206ZEQ | 112630093 | 177166290 | 177166290 | 112630093 | 100 | 56312448 | 0.0012134 | 0.99 | 39.86670 | 38.70032 | 34283660 | 0.342164 | 0.0019487 | 64536197 | 99.99539 | 100 | 38206988 | 85.64 | 49149528 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUHZ302VU4 | 84819581 | 110724093 | 110724093 | 84819581 | 100 | 42407446 | 0.0003190 | 1.00 | 58.77952 | 51.52982 | 28529537 | 0.203833 | 0.0025028 | 25904512 | 99.99447 | 100 | 30685204 | 90.34 | 38920358 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJA217MTJ | 138544788 | 180023548 | 180023548 | 138544788 | 100 | 69268627 | 0.0001135 | 1.01 | 61.97741 | 29.35444 | 26423870 | 0.168603 | 0.0026456 | 41478760 | 99.99456 | 100 | 27865782 | 91.26 | 64185561 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJA666PYD | 104992916 | 179578594 | 179578594 | 104992916 | 100 | 52492856 | 0.0001505 | 0.97 | 42.87717 | 30.33617 | 27240233 | 0.229110 | 0.0027915 | 74585678 | 99.99314 | 100 | 29473424 | 84.84 | 45410352 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJC191RLE | 134351533 | 169112893 | 169112893 | 134351533 | 100 | 67171099 | 0.0004095 | 0.99 | 58.06424 | 36.96069 | 31254937 | 0.244700 | 0.0020588 | 34761360 | 99.99305 | 100 | 33284137 | 90.83 | 62105731 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJG311WGV | 129764735 | 173924387 | 173924387 | 129764735 | 100 | 64879037 | 0.0002634 | 0.98 | 50.35555 | 38.41671 | 33409743 | 0.299301 | 0.0020763 | 44159652 | 99.99487 | 100 | 37635711 | 88.24 | 58253244 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJG885PY7 | 141363192 | 207769282 | 207769282 | 141363192 | 100 | 70672574 | 0.0004961 | 0.99 | 45.29718 | 35.89114 | 37290108 | 0.305882 | 0.0021327 | 66406090 | 99.98724 | 100 | 39751751 | 86.43 | 62682976 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJH197AK2 | 109692064 | 148477602 | 148477602 | 109692064 | 100 | 54840601 | 0.0000835 | 1.01 | 50.42878 | 48.36931 | 35912880 | 0.290581 | 0.0018832 | 38785538 | 99.99010 | 100 | 39219267 | 88.36 | 49489164 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJK720JCL | 145196285 | 176658442 | 176658442 | 145196285 | 100 | 72593038 | 0.0001203 | 0.98 | 58.35053 | 41.40399 | 36574311 | 0.266350 | 0.0022999 | 31462157 | 99.99297 | 100 | 38573347 | 92.26 | 67904327 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJL547WVQ | 122518635 | 147759823 | 147759823 | 122518635 | 100 | 61252132 | 0.0000491 | 1.07 | 56.70514 | 46.87074 | 34632151 | 0.292459 | 0.0018165 | 25241188 | 99.98827 | 100 | 35492615 | 92.56 | 57611614 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJL595JAZ | 125569663 | 167641984 | 167641984 | 125569663 | 100 | 62781255 | 0.0001647 | 1.00 | 49.09008 | 39.12172 | 32794270 | 0.317243 | 0.0024428 | 42072321 | 99.99430 | 100 | 35920670 | 88.09 | 56604191 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJP935AVF | 133932079 | 201524424 | 201524424 | 133932079 | 100 | 66962632 | 0.0004649 | 0.99 | 42.24562 | 30.52310 | 30757338 | 0.337322 | 0.0021899 | 67592345 | 99.99491 | 100 | 34475263 | 85.68 | 58630869 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJX780XXK | 132644761 | 163932667 | 163932667 | 132644761 | 100 | 66316933 | 0.0001693 | 1.00 | 59.09920 | 38.90757 | 31893879 | 0.245205 | 0.0019813 | 31287906 | 99.99179 | 100 | 32976255 | 91.64 | 61928100 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJX990GR5 | 152756972 | 180280188 | 180280188 | 152756972 | 100 | 76370797 | 0.0003500 | 0.98 | 60.56161 | 38.67019 | 34861001 | 0.262740 | 0.0019740 | 27523216 | 99.98993 | 100 | 37160120 | 92.49 | 71699955 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJY426MBU | 163506082 | 212057895 | 212057895 | 163506082 | 100 | 81747885 | 0.0000659 | 0.96 | 55.88217 | 38.63594 | 40967948 | 0.250772 | 0.0019916 | 48551813 | 99.99369 | 100 | 42713301 | 90.91 | 75805318 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUJY536DKF | 130996985 | 161559410 | 161559410 | 130996985 | 100 | 65493732 | 0.0001393 | 0.96 | 59.05377 | 42.66486 | 34467201 | 0.247774 | 0.0020449 | 30562425 | 99.99273 | 100 | 36355288 | 91.51 | 60915279 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUKA860NUG | 95743148 | 149986716 | 149986716 | 95743148 | 100 | 47868100 | 0.0004797 | 0.99 | 39.72778 | 32.51799 | 24388292 | 0.343615 | 0.0022024 | 54243568 | 99.99274 | 100 | 28045765 | 83.39 | 41004845 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUKD025JPF | 73470692 | 95420234 | 95420234 | 73470692 | 100 | 36733163 | 0.0003883 | 1.00 | 61.46689 | 46.42426 | 22150320 | 0.170845 | 0.0026557 | 21949542 | 99.99406 | 100 | 23648413 | 91.00 | 33925482 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUKP160HX8 | 158114922 | 219097462 | 219097462 | 158114922 | 100 | 79053571 | 0.0000658 | 1.00 | 44.77145 | 40.20348 | 44044684 | 0.354843 | 0.0020222 | 60982540 | 99.99508 | 100 | 48852294 | 87.81 | 70714096 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUKR376CW3 | 137592744 | 180066208 | 180066208 | 137592744 | 100 | 68793025 | 0.0002550 | 1.01 | 52.27950 | 38.76256 | 34901012 | 0.291103 | 0.0020278 | 42473464 | 99.99513 | 100 | 37955194 | 89.17 | 62403770 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUKV547CFA | 106270699 | 173079851 | 173079851 | 106270699 | 100 | 53131757 | 0.0001257 | 1.01 | 37.97373 | 32.16386 | 27836633 | 0.347247 | 0.0020279 | 66809152 | 99.99324 | 100 | 32569899 | 82.44 | 45019350 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUKY704JVA | 111957315 | 145492330 | 145492330 | 111957315 | 100 | 55973716 | 0.0006706 | 0.99 | 53.27409 | 44.06555 | 32059068 | 0.281775 | 0.0018965 | 33535015 | 99.99117 | 100 | 34918698 | 88.69 | 51063996 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEULA694DDC | 144121470 | 210976422 | 210976422 | 144121470 | 100 | 72052030 | 0.0001136 | 0.99 | 32.83201 | 39.23243 | 41391076 | 0.496468 | 0.0019312 | 66854952 | 99.98792 | 100 | 46414165 | 85.78 | 63306620 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEULA777DBT | 145235062 | 185554062 | 185554062 | 145235062 | 100 | 72609573 | 0.0001060 | 0.99 | 57.47245 | 38.64274 | 35855491 | 0.238996 | 0.0021044 | 40319000 | 99.98904 | 100 | 37728047 | 90.04 | 66935925 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEULD354RZB | 130303603 | 171222929 | 171222929 | 130303603 | 100 | 65147360 | 0.0000794 | 0.99 | 52.14630 | 39.73101 | 34017084 | 0.290105 | 0.0019778 | 40919326 | 99.99318 | 100 | 37816668 | 88.81 | 58989271 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEULH729AU2 | 132185143 | 188457240 | 188457240 | 132185143 | 100 | 66082206 | 0.0000322 | 1.02 | 33.72764 | 32.90749 | 31013438 | 0.497084 | 0.0022970 | 56272097 | 99.98432 | 100 | 33250669 | 86.85 | 59187708 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEULL588ALG | 101192464 | 129328744 | 129328744 | 101192464 | 100 | 50592428 | 0.0004602 | 1.03 | 62.52614 | 40.65428 | 26290767 | 0.171396 | 0.0025575 | 28136280 | 99.99248 | 100 | 27554179 | 91.05 | 46819320 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEULL648LJ1 | 152013999 | 189349623 | 189349623 | 152013999 | 100 | 75998771 | 0.0003482 | 0.99 | 56.32040 | 46.09657 | 43647051 | 0.275342 | 0.0021868 | 37335624 | 99.98917 | 100 | 47298299 | 90.61 | 70333861 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEULP998KDJ | 101414493 | 129829996 | 129829996 | 101414493 | 100 | 50702318 | 0.0001817 | 1.00 | 57.38737 | 39.83596 | 25862178 | 0.238810 | 0.0019215 | 28415503 | 99.99028 | 100 | 27433069 | 90.22 | 46667209 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEULT851ENP | 141787116 | 182679467 | 182679467 | 141787116 | 100 | 70890034 | 0.0000863 | 0.98 | 52.31735 | 45.64324 | 41692465 | 0.301362 | 0.0019864 | 40892351 | 99.99503 | 100 | 44820562 | 90.51 | 65314488 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEULY177TTN | 88184032 | 140832260 | 140832260 | 88184032 | 100 | 44089217 | 0.0001702 | 0.98 | 45.99328 | 35.86896 | 25258960 | 0.229827 | 0.0026625 | 52648228 | 99.99365 | 100 | 27538571 | 85.82 | 38673250 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEULY328CRJ | 124827649 | 178583027 | 178583027 | 124827649 | 100 | 62409884 | 0.0001362 | 0.99 | 45.38943 | 39.45594 | 35233132 | 0.322612 | 0.0020742 | 53755378 | 99.99369 | 100 | 38907414 | 87.51 | 55659392 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEULZ548ZXV | 116550540 | 157670085 | 157670085 | 116550540 | 100 | 58269845 | 0.0006271 | 1.02 | 50.82802 | 39.63846 | 31252626 | 0.285243 | 0.0021817 | 41119545 | 99.99069 | 100 | 34000171 | 88.43 | 52791572 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUMB242CLN | 146219969 | 188982330 | 188982330 | 146219969 | 100 | 73094377 | 0.0001099 | 0.97 | 53.25336 | 41.38281 | 39111622 | 0.285622 | 0.0020325 | 42762361 | 99.97865 | 100 | 42594423 | 89.14 | 66786201 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUME498PCJ | 121179342 | 166957105 | 166957105 | 121179342 | 100 | 60586895 | 0.0003321 | 0.98 | 53.63860 | 38.22758 | 31913320 | 0.232192 | 0.0024516 | 45777763 | 99.99542 | 100 | 35558756 | 88.60 | 54433039 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUMH634MKT | 149214391 | 209805138 | 209805138 | 149214391 | 100 | 74603299 | 0.0020155 | 1.02 | 46.51324 | 39.06467 | 40982048 | 0.318690 | 0.0020759 | 60590747 | 99.99478 | 100 | 44454595 | 87.85 | 66723213 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUMN012EVP | 122953745 | 152285269 | 152285269 | 122953745 | 100 | 61473583 | 0.0004007 | 0.97 | 60.87585 | 40.63853 | 30944925 | 0.222147 | 0.0019786 | 29331524 | 99.99465 | 100 | 32093482 | 92.10 | 57458694 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUMW598YMT | 148697107 | 211131558 | 211131558 | 148697107 | 100 | 74341725 | 0.0004545 | 0.97 | 45.45767 | 35.42568 | 37401266 | 0.327205 | 0.0021479 | 62434451 | 99.99082 | 100 | 40987087 | 86.39 | 66263817 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUMY871DGF | 139888957 | 164950585 | 164950585 | 139888957 | 100 | 69938355 | 0.0000798 | 0.99 | 64.38220 | 41.02218 | 33836284 | 0.218205 | 0.0019914 | 25061628 | 99.99125 | 100 | 35805638 | 92.48 | 65655990 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUNA248WXL | 87881681 | 112756521 | 112756521 | 87881681 | 100 | 43938255 | 0.0003365 | 0.98 | 63.36786 | 37.94840 | 21395900 | 0.158051 | 0.0026177 | 24874840 | 99.99412 | 100 | 22601559 | 91.86 | 40898290 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUNG326MFP | 141420621 | 188366517 | 188366517 | 141420621 | 100 | 70704595 | 0.0001198 | 0.97 | 51.47303 | 40.77300 | 38404802 | 0.288874 | 0.0019689 | 46945896 | 99.99192 | 100 | 41918606 | 89.03 | 64097084 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUNJ155KYL | 139821585 | 183237512 | 183237512 | 139821585 | 100 | 69907930 | 0.0001016 | 1.03 | 50.34089 | 44.02644 | 40338225 | 0.315424 | 0.0018692 | 43415927 | 99.99591 | 100 | 44436014 | 89.26 | 63359785 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUNJ938DUL | 110373409 | 146981217 | 146981217 | 110373409 | 100 | 55180998 | 0.0002221 | 1.01 | 49.53905 | 42.27752 | 31073805 | 0.313882 | 0.0020983 | 36607808 | 99.98966 | 100 | 34163950 | 87.65 | 49706589 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUNL303HLF | 125099316 | 228966770 | 228966770 | 125099316 | 100 | 62546398 | 0.0001992 | 1.00 | 32.27064 | 29.37712 | 33633585 | 0.378200 | 0.0020683 | 103867454 | 99.99479 | 100 | 36878172 | 82.03 | 52488696 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUNL415AFW | 92867967 | 133667390 | 133667390 | 92867967 | 100 | 46431277 | 0.0008440 | 0.97 | 52.02197 | 42.72272 | 28554762 | 0.219845 | 0.0027121 | 40799423 | 99.99417 | 100 | 30330975 | 88.33 | 41786405 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUNR020KV6 | 115301323 | 164150667 | 164150667 | 115301323 | 100 | 57647868 | 0.0002172 | 0.97 | 46.35115 | 37.01777 | 30383974 | 0.312230 | 0.0020360 | 48849344 | 99.99515 | 100 | 33596521 | 87.46 | 51460383 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUNZ171UYF | 155580787 | 201349190 | 201349190 | 155580787 | 100 | 77786615 | 0.0000477 | 1.00 | 54.53630 | 41.63565 | 41918494 | 0.268249 | 0.0020768 | 45768403 | 99.99514 | 100 | 43804088 | 90.97 | 71885848 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUPG593UTV | 126721699 | 179908913 | 179908913 | 126721699 | 100 | 63355853 | 0.0002942 | 0.98 | 43.44807 | 36.26768 | 32627194 | 0.356489 | 0.0021263 | 53187214 | 99.99211 | 100 | 36485890 | 86.39 | 56098842 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUPK546ZLD | 127719209 | 173514278 | 173514278 | 127719209 | 100 | 63853530 | 0.0006982 | 0.98 | 52.70728 | 41.76322 | 36236208 | 0.255609 | 0.0019434 | 45795069 | 99.99049 | 100 | 38892514 | 88.95 | 58161535 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUPM937TMY | 114752546 | 154017532 | 154017532 | 114752546 | 100 | 57373291 | 0.0001371 | 1.00 | 48.91011 | 40.73999 | 31375051 | 0.317677 | 0.0020453 | 39264986 | 99.99480 | 100 | 33677004 | 89.09 | 52119903 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUPN525XEW | 100061085 | 152901938 | 152901938 | 100061085 | 100 | 50027523 | 0.0011091 | 0.96 | 48.26096 | 37.85523 | 28942287 | 0.229381 | 0.0027257 | 52840853 | 99.99396 | 100 | 30587704 | 86.88 | 44430092 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUPR357AUF | 140600115 | 188629695 | 188629695 | 140600115 | 100 | 70294764 | 0.0003826 | 1.01 | 50.96441 | 42.12141 | 39730312 | 0.290189 | 0.0020325 | 48029580 | 99.99247 | 100 | 42959648 | 88.51 | 63541475 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUPR600MBU | 101661612 | 157059475 | 157059475 | 101661612 | 100 | 50828202 | 0.0006545 | 0.95 | 47.55700 | 38.91106 | 30558182 | 0.231348 | 0.0025577 | 55397863 | 99.99488 | 100 | 33189766 | 87.17 | 45072415 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUPY050ANK | 125092895 | 173092975 | 173092975 | 125092895 | 100 | 62538321 | 0.0008399 | 0.97 | 47.48535 | 37.00170 | 32028248 | 0.316107 | 0.0021859 | 48000080 | 99.98701 | 100 | 34791092 | 87.00 | 56250544 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEURA639MK8 | 88681385 | 174800313 | 174800313 | 88681385 | 100 | 44338192 | 0.0002404 | 0.99 | 35.38047 | 26.17944 | 22881914 | 0.261938 | 0.0026667 | 86118928 | 99.99436 | 100 | 25273046 | 81.23 | 36696280 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEURF720KHA | 127645475 | 214650164 | 214650164 | 127645475 | 100 | 63818250 | 0.0001552 | 1.02 | 37.19388 | 30.61430 | 32858913 | 0.341368 | 0.0020499 | 87004689 | 99.99297 | 100 | 36233250 | 84.23 | 54948319 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEURJ362MXH | 128821381 | 164937784 | 164937784 | 128821381 | 100 | 64406009 | 0.0002776 | 0.99 | 54.82691 | 32.31893 | 26655251 | 0.273043 | 0.0020595 | 36116403 | 99.99273 | 100 | 28257434 | 90.79 | 59538230 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEURR881FKY | 107640056 | 139900164 | 139900164 | 107640056 | 100 | 53817142 | 0.0001954 | 0.97 | 59.88210 | 38.77847 | 27126995 | 0.192805 | 0.0024546 | 32260108 | 99.99464 | 100 | 29184368 | 90.84 | 49514621 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEURX315DYH | 105760532 | 182500083 | 182500083 | 105760532 | 100 | 52875618 | 0.0002318 | 1.00 | 38.24761 | 32.14216 | 29332003 | 0.304415 | 0.0019613 | 76739551 | 99.99121 | 100 | 31862596 | 84.81 | 45743652 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEURX909UL6 | 101253707 | 143049397 | 143049397 | 101253707 | 100 | 50623663 | 0.0003391 | 0.99 | 52.97698 | 43.28501 | 30961318 | 0.218807 | 0.0026655 | 41795690 | 99.99370 | 100 | 33363015 | 88.75 | 45735585 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTA057AF6 | 145972936 | 182832898 | 182832898 | 145972936 | 100 | 72981892 | 0.0001730 | 0.98 | 57.41441 | 42.36811 | 38733887 | 0.255461 | 0.0019554 | 36859962 | 99.99373 | 100 | 39947509 | 92.03 | 68030270 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTA689LN5 | 97978631 | 137960489 | 137960489 | 97978631 | 100 | 48986369 | 0.0000766 | 0.99 | 54.36726 | 45.44476 | 31349678 | 0.201869 | 0.0026863 | 39981858 | 99.99399 | 100 | 33057528 | 89.27 | 44471077 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTB230DA3 | 127287620 | 167555194 | 167555194 | 127287620 | 100 | 63638375 | 0.0002299 | 0.99 | 51.77864 | 44.64902 | 37410054 | 0.293582 | 0.0021534 | 40267574 | 99.99146 | 100 | 41078024 | 88.53 | 57735990 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTC791PVE | 145218429 | 194002781 | 194002781 | 145218429 | 100 | 72602394 | 0.0001546 | 0.96 | 48.45311 | 42.66868 | 41393810 | 0.326557 | 0.0020144 | 48784352 | 99.99061 | 100 | 45961276 | 87.67 | 65228107 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTD314VFT | 118694774 | 199503383 | 199503383 | 118694774 | 100 | 59340190 | 0.0003396 | 1.01 | 40.55880 | 28.63025 | 28562306 | 0.283515 | 0.0019801 | 80808609 | 99.98787 | 100 | 31769329 | 84.10 | 51072663 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTD713DE3 | 111654521 | 157067140 | 157067140 | 111654521 | 100 | 55824002 | 0.0001290 | 0.98 | 52.91439 | 42.42968 | 33323420 | 0.224722 | 0.0027149 | 45412619 | 99.99416 | 100 | 35928817 | 89.06 | 50602796 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTD866EAH | 124436305 | 180663402 | 180663402 | 124436305 | 100 | 62210277 | 0.0002514 | 0.98 | 44.24790 | 38.73755 | 34997730 | 0.329244 | 0.0021389 | 56227097 | 99.98734 | 100 | 39272084 | 85.83 | 54881137 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTJ613AH9 | 72472964 | 98310077 | 98310077 | 72472964 | 100 | 36233970 | 0.0002277 | 0.99 | 59.58567 | 35.73748 | 17567925 | 0.161272 | 0.0026973 | 25837113 | 99.99307 | 100 | 18303686 | 90.13 | 33289122 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTL257PNR | 132701657 | 180494960 | 180494960 | 132701657 | 100 | 66347623 | 0.0002861 | 1.00 | 49.20961 | 39.11086 | 35298356 | 0.304793 | 0.0020186 | 47793303 | 99.99517 | 100 | 37791840 | 88.97 | 60066049 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTL699WJ0 | 114658516 | 144969594 | 144969594 | 114658516 | 100 | 57324735 | 0.0010707 | 0.97 | 56.07008 | 44.57791 | 32315111 | 0.266599 | 0.0019060 | 30311078 | 99.99211 | 100 | 35710392 | 89.86 | 52348367 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTM934BPY | 129527421 | 171464767 | 171464767 | 129527421 | 100 | 64759198 | 0.0015967 | 1.00 | 53.80390 | 36.74346 | 31503263 | 0.261451 | 0.0020043 | 41937346 | 99.99303 | 100 | 34456215 | 89.53 | 59086995 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTN952DDG | 105873411 | 166179344 | 166179344 | 105873411 | 100 | 52933748 | 0.0003591 | 0.99 | 46.94140 | 33.50951 | 27844308 | 0.231224 | 0.0025588 | 60305933 | 99.99441 | 100 | 29696227 | 86.83 | 46944485 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUTU360YJY | 116118985 | 143509356 | 143509356 | 116118985 | 100 | 58052735 | 0.0001467 | 1.01 | 57.95106 | 53.19941 | 38177862 | 0.259297 | 0.0017220 | 27390371 | 99.98836 | 100 | 41726408 | 90.06 | 53322943 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUC458RFT | 129847013 | 194034481 | 194034481 | 129847013 | 100 | 64917516 | 0.0001199 | 1.02 | 41.97888 | 34.38410 | 33362263 | 0.343356 | 0.0020920 | 64187468 | 99.99077 | 100 | 37273830 | 84.20 | 56817414 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUD158CJF | 104670750 | 132835531 | 132835531 | 104670750 | 100 | 52328344 | 0.0000158 | 0.97 | 53.12357 | 47.52401 | 31569214 | 0.300438 | 0.0018088 | 28164781 | 99.98657 | 100 | 35081615 | 88.71 | 47698947 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUE852BB1 | 87313527 | 122251990 | 122251990 | 87313527 | 100 | 43654085 | 0.0000895 | 0.98 | 54.63034 | 43.88646 | 26827563 | 0.201953 | 0.0025186 | 34938463 | 99.99386 | 100 | 28952491 | 88.87 | 39423970 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUF613PHL | 126490792 | 162878061 | 162878061 | 126490792 | 100 | 63241442 | 0.0000430 | 0.97 | 52.54516 | 42.82306 | 34877131 | 0.298866 | 0.0021813 | 36387269 | 99.99375 | 100 | 38470412 | 89.41 | 57733762 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUH658EYH | 121126070 | 181119012 | 181119012 | 121126070 | 100 | 60560176 | 0.0006071 | 1.00 | 41.82229 | 39.10448 | 35414672 | 0.346869 | 0.0019553 | 59992942 | 99.99528 | 100 | 40091692 | 85.86 | 53030800 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUJ507EAB | 114321103 | 144750000 | 144750000 | 114321103 | 100 | 57157204 | 0.0000440 | 1.06 | 53.63220 | 47.14457 | 34123017 | 0.296042 | 0.0015816 | 30428897 | 99.99414 | 100 | 37643813 | 89.78 | 52034154 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUL256UC9 | 119837015 | 165056579 | 165056579 | 119837015 | 100 | 59911454 | 0.0001191 | 0.98 | 53.36755 | 30.51364 | 25185391 | 0.235516 | 0.0021328 | 45219564 | 99.98823 | 100 | 27258314 | 87.95 | 54168228 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUL292XRC | 104836431 | 156852741 | 156852741 | 104836431 | 100 | 52409181 | 0.0003069 | 1.00 | 43.89086 | 33.23504 | 26069986 | 0.311924 | 0.0019622 | 52016310 | 99.98276 | 100 | 29882387 | 84.80 | 45819278 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUL311NRQ | 144461771 | 187508051 | 187508051 | 144461771 | 100 | 72226897 | 0.0001483 | 1.03 | 51.75003 | 41.70654 | 39103731 | 0.303675 | 0.0019373 | 43046280 | 99.99448 | 100 | 42363669 | 90.08 | 66008915 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUP280KXL | 118516272 | 156079810 | 156079810 | 118516272 | 100 | 59254381 | 0.0001999 | 0.99 | 54.93796 | 41.02595 | 32018652 | 0.250312 | 0.0019529 | 37563538 | 99.99366 | 100 | 33948150 | 89.62 | 54110646 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUU506WZF | 138573134 | 292249673 | 292249673 | 138573134 | 100 | 69279224 | 0.0006337 | 0.99 | 29.33627 | 18.68155 | 27300803 | 0.342525 | 0.0023071 | 153676539 | 99.98940 | 100 | 30195009 | 78.78 | 56290277 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUUZ216XY8 | 117115830 | 153394704 | 153394704 | 117115830 | 100 | 58553043 | 0.0003654 | 1.01 | 53.12807 | 42.10338 | 32295500 | 0.276408 | 0.0019538 | 36278874 | 99.99168 | 100 | 35552913 | 89.03 | 53409559 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVD687XD8 | 127850466 | 196983862 | 196983862 | 127850466 | 100 | 63918317 | 0.0002929 | 1.01 | 41.30500 | 33.27007 | 32772166 | 0.333570 | 0.0022399 | 69133396 | 99.98918 | 100 | 36669301 | 84.14 | 55483568 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVF888UHM | 87839503 | 123440383 | 123440383 | 87839503 | 100 | 43916958 | 0.0008791 | 1.01 | 55.05094 | 38.51858 | 23775161 | 0.194150 | 0.0027037 | 35600880 | 99.99364 | 100 | 25076486 | 88.39 | 39713751 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVJ560JGZ | 145026604 | 169004770 | 169004770 | 145026604 | 100 | 72508859 | 0.0001747 | 0.99 | 66.23438 | 37.93196 | 32055485 | 0.205332 | 0.0020462 | 23978166 | 99.99387 | 100 | 32639281 | 93.31 | 68598571 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVM674HUA | 112397326 | 158281937 | 158281937 | 112397326 | 100 | 56194993 | 0.0001695 | 1.00 | 50.24582 | 44.73241 | 35403908 | 0.263150 | 0.0026860 | 45884611 | 99.99347 | 100 | 38967578 | 87.97 | 50368377 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVN746WKV | 113418563 | 166319216 | 166319216 | 113418563 | 100 | 56705806 | 0.0000901 | 1.00 | 48.88816 | 38.69327 | 32179025 | 0.250970 | 0.0026661 | 52900653 | 99.99387 | 100 | 34899811 | 87.12 | 50451695 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVP060WFG | 144863978 | 187399644 | 187399644 | 144863978 | 100 | 72426514 | 0.0000170 | 0.99 | 49.74931 | 43.87856 | 41117626 | 0.333074 | 0.0020505 | 42535666 | 99.99244 | 100 | 45474655 | 88.88 | 65686991 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVR636VTP | 128629292 | 171359932 | 171359932 | 128629292 | 100 | 64309737 | 0.0001487 | 1.00 | 53.73263 | 38.45949 | 32954754 | 0.258677 | 0.0020067 | 42730640 | 99.99237 | 100 | 35787049 | 89.32 | 58705014 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVR814YCY | 144773359 | 197542865 | 197542865 | 144773359 | 100 | 72382408 | 0.0004202 | 1.00 | 50.77449 | 33.73113 | 33318593 | 0.281012 | 0.0023057 | 52769506 | 99.99410 | 100 | 34471604 | 89.47 | 65992995 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVU735HU6 | 123502082 | 187698709 | 187698709 | 123502082 | 100 | 61747675 | 0.0003588 | 0.99 | 42.95702 | 34.74852 | 32612974 | 0.315037 | 0.0023181 | 64196627 | 99.99455 | 100 | 34653270 | 86.96 | 54922335 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVV225XKB | 123111385 | 155952079 | 155952079 | 123111385 | 100 | 61551693 | 0.0003383 | 1.00 | 54.53868 | 45.87263 | 35772048 | 0.283807 | 0.0020836 | 32840694 | 99.99350 | 100 | 37689921 | 91.00 | 56974263 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVW680LPK | 118581069 | 153225477 | 153225477 | 118581069 | 100 | 59284066 | 0.0003044 | 0.99 | 55.01467 | 45.87971 | 35153671 | 0.262525 | 0.0018957 | 34644408 | 99.98909 | 100 | 38389290 | 89.49 | 54123971 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVW999FP9 | 122111979 | 175530863 | 175530863 | 122111979 | 100 | 61050651 | 0.0000599 | 1.00 | 48.28043 | 41.87448 | 36754568 | 0.275443 | 0.0018434 | 53418884 | 99.99126 | 100 | 39758243 | 87.43 | 54642824 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUVX902YNL | 105687552 | 141270293 | 141270293 | 105687552 | 100 | 52838977 | 0.0003394 | 0.95 | 55.41355 | 31.70045 | 22393705 | 0.231272 | 0.0019910 | 35582741 | 99.99092 | 100 | 24062627 | 89.75 | 48398706 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUWD538KT3 | 93128892 | 129580487 | 129580487 | 93128892 | 100 | 46561423 | 0.0001520 | 0.97 | 55.12257 | 46.72140 | 30272812 | 0.202011 | 0.0025389 | 36451595 | 99.99351 | 100 | 32314676 | 89.32 | 42289028 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUWD946RDA | 149520819 | 197641724 | 197641724 | 149520819 | 100 | 74753779 | 0.0002987 | 0.96 | 49.86001 | 43.02003 | 42517032 | 0.316072 | 0.0020719 | 48120905 | 99.99113 | 100 | 45622870 | 88.81 | 68185631 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUWH380YHV | 118758017 | 154302029 | 154302029 | 118758017 | 100 | 59375307 | 0.0002332 | 0.99 | 56.59547 | 42.23046 | 32583607 | 0.238610 | 0.0018427 | 35544012 | 99.99377 | 100 | 34472568 | 90.88 | 54730470 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUWH955FJF | 130639547 | 170232499 | 170232499 | 130639547 | 100 | 65312616 | 0.0001261 | 1.01 | 51.82487 | 39.11938 | 33300864 | 0.300246 | 0.0022484 | 39592952 | 99.98904 | 100 | 36381430 | 89.03 | 59642239 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUWJ389FC7 | 120192862 | 150666058 | 150666058 | 120192862 | 100 | 60092014 | 0.0000771 | 0.99 | 57.07302 | 43.05931 | 32440780 | 0.260635 | 0.0019176 | 30473196 | 99.99265 | 100 | 34827714 | 90.90 | 55551131 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUWM344ZLM | 117831195 | 162934462 | 162934462 | 117831195 | 100 | 58912499 | 0.0002679 | 0.99 | 47.54644 | 36.20085 | 29493516 | 0.317124 | 0.0020166 | 45103267 | 99.99474 | 100 | 33397586 | 87.79 | 52677231 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUWP426NBR | 104117727 | 136600495 | 136600495 | 104117727 | 100 | 52055846 | 0.0001242 | 0.95 | 60.07319 | 40.07443 | 27372491 | 0.182672 | 0.0026510 | 32482768 | 99.99420 | 100 | 28549535 | 90.96 | 48071230 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUWX167DAH | 123682005 | 192704366 | 192704366 | 123682005 | 100 | 61834940 | 0.0001177 | 1.00 | 43.57415 | 37.02141 | 35674317 | 0.289182 | 0.0018338 | 69022361 | 99.99020 | 100 | 39765447 | 85.55 | 54107517 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUWY079WUH | 129106543 | 181255681 | 181255681 | 129106543 | 100 | 64541424 | 0.0003487 | 0.98 | 40.01595 | 37.65129 | 34129175 | 0.412852 | 0.0023745 | 52149138 | 99.98165 | 100 | 36559926 | 87.00 | 58040835 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUWZ614ARQ | 106843000 | 145508107 | 145508107 | 106843000 | 100 | 53419244 | 0.0002842 | 0.99 | 47.92555 | 42.08033 | 30616507 | 0.320886 | 0.0020071 | 38665107 | 99.99578 | 100 | 33688160 | 88.80 | 48202453 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUXD985ZU1 | 140301006 | 196956825 | 196956825 | 140301006 | 100 | 70146701 | 0.0000676 | 0.99 | 45.17465 | 36.03483 | 35488642 | 0.339938 | 0.0021713 | 56655819 | 99.99458 | 100 | 38729715 | 87.42 | 62695888 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUXE491RMM | 97865811 | 118906208 | 118906208 | 97865811 | 100 | 48930212 | 0.0002695 | 0.98 | 66.82962 | 45.56580 | 27091815 | 0.161633 | 0.0026411 | 21040397 | 99.99450 | 100 | 28413979 | 92.38 | 45870390 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUXG265ME9 | 129621756 | 168423467 | 168423467 | 129621756 | 100 | 64806369 | 0.0005600 | 1.00 | 53.74925 | 41.77200 | 35179399 | 0.275283 | 0.0019760 | 38801711 | 99.99304 | 100 | 37190260 | 90.24 | 59421241 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUXH833LL4 | 142418106 | 190308209 | 190308209 | 142418106 | 100 | 71203163 | 0.0004520 | 1.01 | 50.06242 | 45.10139 | 42919477 | 0.306045 | 0.0020634 | 47890103 | 99.99173 | 100 | 46255615 | 89.75 | 65035209 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUXP289KRC | 137919894 | 180193491 | 180193491 | 137919894 | 100 | 68955155 | 0.0000422 | 0.98 | 56.83071 | 36.80424 | 33161771 | 0.230765 | 0.0020719 | 42273597 | 99.99305 | 100 | 33565706 | 91.30 | 64019350 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUXP495XE2 | 144883140 | 207898467 | 207898467 | 144883140 | 100 | 72437782 | 0.0005885 | 0.99 | 46.52462 | 35.14467 | 36534422 | 0.305425 | 0.0021574 | 63015327 | 99.99477 | 100 | 38386537 | 87.90 | 64915635 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUXP595FFP | 82882330 | 112629927 | 112629927 | 82882330 | 100 | 41439054 | 0.0004402 | 0.97 | 57.41643 | 43.96293 | 24758914 | 0.187966 | 0.0024695 | 29747597 | 99.99491 | 100 | 26423196 | 90.13 | 37877172 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUXV122FN3 | 128046620 | 164194973 | 164194973 | 128046620 | 100 | 64017537 | 0.0001862 | 1.00 | 55.16521 | 46.44593 | 38134683 | 0.267302 | 0.0018444 | 36148353 | 99.99098 | 100 | 41583014 | 89.72 | 58733300 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUXX361RUG | 107229021 | 133348579 | 133348579 | 107229021 | 100 | 53611368 | 0.0003016 | 0.99 | 63.68358 | 48.23219 | 32160375 | 0.181221 | 0.0026846 | 26119558 | 99.99414 | 100 | 33003046 | 92.07 | 50204894 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYC055XPZ | 138951866 | 173601788 | 173601788 | 138951866 | 100 | 69470318 | 0.0001920 | 0.99 | 55.76776 | 40.19634 | 34893729 | 0.279873 | 0.0020410 | 34649922 | 99.99192 | 100 | 37040582 | 91.22 | 64543705 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYC303AJY | 120708861 | 161874054 | 161874054 | 120708861 | 100 | 60350667 | 0.0004616 | 0.98 | 51.12615 | 39.61285 | 32063539 | 0.286988 | 0.0021230 | 41165193 | 99.99376 | 100 | 34113253 | 90.06 | 55283224 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYD306HAB | 127940942 | 182627299 | 182627299 | 127940942 | 100 | 63946168 | 0.0002491 | 1.01 | 36.74887 | 40.42930 | 36932268 | 0.451589 | 0.0019820 | 54686357 | 99.96201 | 100 | 42007862 | 83.18 | 56076091 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYG208KVV | 124891243 | 199498682 | 199498682 | 124891243 | 100 | 62442357 | 0.0001144 | 0.99 | 38.73081 | 31.53442 | 31456954 | 0.351701 | 0.0021026 | 74607439 | 99.99477 | 100 | 35299541 | 84.26 | 54046799 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYG298CA9 | 123272477 | 157809619 | 157809619 | 123272477 | 100 | 61632259 | 0.0002451 | 0.97 | 53.71753 | 48.08596 | 37944789 | 0.287246 | 0.0019546 | 34537142 | 99.99354 | 100 | 41968903 | 89.21 | 55941940 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYH924UCE | 119170920 | 163713959 | 163713959 | 119170920 | 100 | 59578923 | 0.0002091 | 1.00 | 52.69253 | 39.72040 | 32517623 | 0.248715 | 0.0020415 | 44543039 | 99.98903 | 100 | 34070517 | 88.79 | 54150809 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYJ705VN9 | 122863974 | 178270837 | 178270837 | 122863974 | 100 | 61425993 | 0.0001050 | 0.98 | 44.63852 | 38.44930 | 34275732 | 0.324227 | 0.0022001 | 55406863 | 99.99024 | 100 | 37266516 | 85.92 | 54518769 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYK029WUU | 89122275 | 114077752 | 114077752 | 89122275 | 100 | 44558477 | 0.0000914 | 0.97 | 61.38720 | 46.04638 | 26265846 | 0.185776 | 0.0024906 | 24955477 | 99.99403 | 100 | 28032018 | 90.95 | 41147531 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYL008GM4 | 111596389 | 136189939 | 136189939 | 111596389 | 100 | 55793552 | 0.0001722 | 0.97 | 68.59611 | 32.41083 | 22071962 | 0.135216 | 0.0028679 | 24593550 | 99.99168 | 100 | 22785219 | 92.39 | 52394355 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYL149PRF | 108007117 | 135498385 | 135498385 | 108007117 | 100 | 54000728 | 0.0002878 | 0.98 | 61.14424 | 53.84660 | 36482547 | 0.206587 | 0.0025245 | 27491268 | 99.99476 | 100 | 38738756 | 91.11 | 50062588 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYP226CPW | 140904052 | 200107332 | 200107332 | 140904052 | 100 | 70445538 | 0.0001431 | 1.02 | 45.97181 | 39.80486 | 39830197 | 0.319377 | 0.0018772 | 59203280 | 99.99079 | 100 | 43697397 | 86.71 | 62985933 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYP235ZLD | 112041837 | 154018964 | 154018964 | 112041837 | 100 | 56012285 | 0.0006468 | 0.98 | 53.34704 | 30.31082 | 23345849 | 0.236692 | 0.0022270 | 41977127 | 99.98459 | 100 | 24774214 | 88.37 | 50797298 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYT193FFG | 135937514 | 167443145 | 167443145 | 135937514 | 100 | 67965213 | 0.0002058 | 0.99 | 55.17711 | 45.26622 | 37899750 | 0.298018 | 0.0020057 | 31505631 | 99.99479 | 100 | 40441406 | 91.04 | 62909433 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYY225MNZ | 86663158 | 113081381 | 113081381 | 86663158 | 100 | 43329287 | 0.0000491 | 0.97 | 61.57635 | 43.19503 | 24424016 | 0.168417 | 0.0025204 | 26418223 | 99.99471 | 100 | 25706055 | 91.35 | 40143805 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYY614DN8 | 143420041 | 207828429 | 207828429 | 143420041 | 100 | 71705432 | 0.0001386 | 0.98 | 43.48929 | 38.17697 | 39674516 | 0.341201 | 0.0021712 | 64408388 | 99.99360 | 100 | 44205920 | 85.74 | 63160903 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUYY878JGP | 133161137 | 172765129 | 172765129 | 133161137 | 100 | 66576125 | 0.0004581 | 0.99 | 54.69875 | 45.73749 | 39512171 | 0.264335 | 0.0020122 | 39603992 | 99.99333 | 100 | 41230805 | 90.43 | 61407501 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZD231YZ6 | 114115577 | 160409162 | 160409162 | 114115577 | 100 | 57054121 | 0.0003026 | 0.98 | 37.42191 | 39.14512 | 31398709 | 0.450324 | 0.0020169 | 46293585 | 99.99357 | 100 | 35064123 | 87.49 | 50905501 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZE432DZM | 130181306 | 183450507 | 183450507 | 130181306 | 100 | 65085949 | 0.0000718 | 0.98 | 46.85383 | 39.45448 | 36192628 | 0.311264 | 0.0019646 | 53269201 | 99.99277 | 100 | 40115753 | 87.01 | 57917361 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZF321EW4 | 137296801 | 237074262 | 237074262 | 137296801 | 100 | 68645200 | 0.0004753 | 1.01 | 35.69136 | 28.75297 | 34084476 | 0.352639 | 0.0019988 | 99777461 | 99.99534 | 100 | 38615057 | 83.54 | 58499666 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZF473UEP | 115673202 | 160994953 | 160994953 | 115673202 | 100 | 57829951 | 0.0005352 | 0.98 | 47.71084 | 36.89973 | 29707207 | 0.306990 | 0.0021394 | 45321751 | 99.98850 | 100 | 33058534 | 86.18 | 51678195 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZJ053JGZ | 133079937 | 177519663 | 177519663 | 133079937 | 100 | 66536354 | 0.0003317 | 1.00 | 49.27551 | 37.35663 | 33159728 | 0.317630 | 0.0020517 | 44439726 | 99.99457 | 100 | 36138181 | 88.41 | 59979953 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZK054DP5 | 120214668 | 154653148 | 154653148 | 120214668 | 100 | 60103402 | 0.0004124 | 1.04 | 52.53178 | 45.78244 | 35404472 | 0.298436 | 0.0018783 | 34438480 | 99.99346 | 100 | 38496742 | 89.95 | 54950104 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZN836GME | 145980665 | 199472112 | 199472112 | 145980665 | 100 | 72983931 | 0.0002882 | 1.01 | 52.13303 | 42.78780 | 42678756 | 0.260984 | 0.0020023 | 53491447 | 99.99123 | 100 | 44497522 | 89.27 | 66523707 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZN936HJ9 | 81372630 | 106601993 | 106601993 | 81372630 | 100 | 40681058 | 0.0003806 | 1.00 | 55.49972 | 40.91089 | 21809049 | 0.244893 | 0.0018392 | 25229363 | 99.98708 | 100 | 23946737 | 86.35 | 37033610 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZP278MR4 | 131323891 | 176068176 | 176068176 | 131323891 | 100 | 65655018 | 0.0006721 | 1.01 | 51.81335 | 37.00994 | 32585406 | 0.279093 | 0.0019754 | 44744285 | 99.98945 | 100 | 35651501 | 88.06 | 59272066 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZT557DHF | 106461904 | 143299163 | 143299163 | 106461904 | 100 | 53227723 | 0.0003853 | 0.97 | 58.32994 | 40.20927 | 28811446 | 0.184961 | 0.0026631 | 36837259 | 99.99393 | 100 | 30130126 | 90.24 | 48805126 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZT902WVB | 148124441 | 182236026 | 182236026 | 148124441 | 100 | 74058202 | 0.0000503 | 0.98 | 57.46045 | 43.65235 | 39777357 | 0.269224 | 0.0021408 | 34111585 | 99.99457 | 100 | 42140814 | 91.69 | 68930822 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZV656DD1 | 148595712 | 191967771 | 191967771 | 148595712 | 100 | 74290018 | 0.0002922 | 1.01 | 53.56322 | 40.64046 | 39012951 | 0.283583 | 0.0019968 | 43372059 | 99.98945 | 100 | 42775759 | 89.23 | 67818461 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZW701NNF | 103881710 | 161910752 | 161910752 | 103881710 | 100 | 51938334 | 0.0004089 | 0.99 | 38.59967 | 33.83292 | 27390995 | 0.370488 | 0.0018256 | 58029042 | 99.99515 | 100 | 31808231 | 84.18 | 44505268 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZX521TKK | 98509768 | 147866623 | 147866623 | 98509768 | 100 | 49251743 | 0.0011162 | 0.99 | 49.59044 | 37.31938 | 27593127 | 0.221318 | 0.0025534 | 49356855 | 99.99362 | 100 | 30499773 | 86.53 | 43500814 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZX847VWV | 119842527 | 151675489 | 151675489 | 119842527 | 100 | 59914634 | 0.0005850 | 0.99 | 57.32521 | 42.14669 | 31967012 | 0.249421 | 0.0019800 | 31832962 | 99.98894 | 100 | 34686632 | 89.97 | 55085136 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZY128BJ2 | 150783455 | 204326818 | 204326818 | 150783455 | 100 | 75386092 | 0.0001938 | 0.96 | 48.60244 | 37.88189 | 38704461 | 0.315447 | 0.0020149 | 53543363 | 99.99253 | 100 | 42610444 | 88.01 | 67775270 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CASE_NEUZY975XKL | 109304246 | 144951033 | 144951033 | 109304246 | 100 | 54649315 | 0.0001080 | 1.02 | 50.04858 | 47.28401 | 34271213 | 0.310375 | 0.0018150 | 35646787 | 99.99486 | 100 | 38548384 | 88.36 | 48940600 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUAA485DZL | 142730071 | 206651342 | 206651342 | 142730071 | 100 | 71358075 | 0.0001363 | 1.01 | 42.96172 | 40.46539 | 41815801 | 0.350993 | 0.0019086 | 63921271 | 99.99025 | 100 | 46974414 | 85.30 | 62633765 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUAJ025JC3 | 95976943 | 127242318 | 127242318 | 95976943 | 100 | 47985999 | 0.0002535 | 0.98 | 59.67276 | 40.91501 | 26031923 | 0.178385 | 0.0026401 | 31265375 | 99.99485 | 100 | 27673100 | 90.71 | 44173605 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUAJ928PAA | 119849155 | 148067308 | 148067308 | 119849155 | 100 | 59920487 | 0.0000620 | 0.98 | 63.17580 | 50.11523 | 37104650 | 0.193182 | 0.0026209 | 28218153 | 99.99317 | 100 | 39200380 | 91.47 | 55771640 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUCA748GF2 | 107664405 | 137518200 | 137518200 | 107664405 | 100 | 53827862 | 0.0002251 | 0.98 | 57.66832 | 32.94083 | 22651817 | 0.238273 | 0.0020644 | 29853795 | 99.99194 | 100 | 24571396 | 89.73 | 49288757 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUCV136DHM | 133777770 | 169397330 | 169397330 | 133777770 | 100 | 66882436 | 0.0000651 | 0.99 | 55.08695 | 48.92659 | 41444984 | 0.278311 | 0.0018345 | 35619560 | 99.99036 | 100 | 45549599 | 89.72 | 61182809 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUCV809LL4 | 75164929 | 112702935 | 112702935 | 75164929 | 100 | 37579947 | 0.0003591 | 0.99 | 51.05006 | 34.10042 | 19217322 | 0.199274 | 0.0029202 | 37538006 | 99.99330 | 100 | 20568369 | 87.18 | 33519005 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUDA782GW3 | 84711501 | 107695370 | 107695370 | 84711501 | 100 | 42353186 | 0.0000815 | 1.00 | 63.74855 | 38.74052 | 20862147 | 0.160241 | 0.0026666 | 22983869 | 99.99395 | 100 | 21427666 | 91.81 | 39438521 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUDE949BP3 | 106950527 | 160325830 | 160325830 | 106950527 | 100 | 53472417 | 0.0004657 | 0.97 | 50.28890 | 37.22890 | 29845269 | 0.213953 | 0.0025578 | 53375303 | 99.99468 | 100 | 31526501 | 88.57 | 48108748 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUDM126GNG | 109647418 | 144319019 | 144319019 | 109647418 | 100 | 54820128 | 0.0000840 | 0.98 | 59.50635 | 44.56285 | 32158364 | 0.185721 | 0.0027073 | 34671601 | 99.99347 | 100 | 34382218 | 89.76 | 50168400 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUDT762KUL | 104193773 | 168014070 | 168014070 | 104193773 | 100 | 52094773 | 0.0003644 | 1.00 | 39.04926 | 32.66405 | 27441220 | 0.338047 | 0.0021123 | 63820297 | 99.99594 | 100 | 30288348 | 85.30 | 45243066 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUEB210XRC | 126699869 | 166317212 | 166317212 | 126699869 | 100 | 63340865 | 0.0003199 | 1.00 | 48.59671 | 45.47978 | 37826434 | 0.338585 | 0.0019693 | 39617343 | 99.98568 | 100 | 42145092 | 87.81 | 57006910 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUEY565NWT | 99688142 | 135142105 | 135142105 | 99688142 | 100 | 49840653 | 0.0002137 | 1.00 | 58.78130 | 40.86577 | 27615249 | 0.170502 | 0.0026984 | 35453963 | 99.99314 | 100 | 29065895 | 90.01 | 45685875 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUFL733GX5 | 123100513 | 163533801 | 163533801 | 123100513 | 100 | 61545257 | 0.0002462 | 1.02 | 55.30460 | 38.73854 | 31677879 | 0.236233 | 0.0020375 | 40433288 | 99.99188 | 100 | 32733496 | 90.31 | 56609176 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUFZ500KDB | 105364734 | 144983815 | 144983815 | 105364734 | 100 | 52678661 | 0.0001249 | 0.99 | 56.25394 | 40.86537 | 29626090 | 0.192852 | 0.0028539 | 39619081 | 99.99297 | 100 | 31637441 | 89.34 | 47960440 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUFZ508VBV | 92018121 | 113000997 | 113000997 | 92018121 | 100 | 46006716 | 0.0000357 | 1.01 | 64.99242 | 44.63934 | 25222765 | 0.175065 | 0.0025146 | 20982876 | 99.99490 | 100 | 26953022 | 92.14 | 42988984 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUHE723FGT | 125537737 | 162056376 | 162056376 | 125537737 | 100 | 62764270 | 0.0011938 | 0.98 | 58.65879 | 32.97615 | 26721907 | 0.215906 | 0.0021614 | 36518639 | 99.99267 | 100 | 26793823 | 90.97 | 58252831 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUHZ716BZ2 | 85710543 | 111187686 | 111187686 | 85710543 | 100 | 42852487 | 0.0002070 | 0.96 | 61.79334 | 39.97116 | 22222904 | 0.169172 | 0.0028450 | 25477143 | 99.99350 | 100 | 23292684 | 90.31 | 39527760 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUJH290RH7 | 82173096 | 118342717 | 118342717 | 82173096 | 100 | 41084532 | 0.0001731 | 0.99 | 54.19480 | 36.11641 | 21371505 | 0.186395 | 0.0025146 | 36169621 | 99.99509 | 100 | 23245087 | 88.94 | 37082361 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUJX341NDP | 86296043 | 112040549 | 112040549 | 86296043 | 100 | 43145527 | 0.0001699 | 0.95 | 61.72160 | 36.76733 | 20598281 | 0.169698 | 0.0026220 | 25744506 | 99.99422 | 100 | 21891892 | 90.82 | 39861968 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUKW131XJ2 | 95809608 | 136890063 | 136890063 | 95809608 | 100 | 47902177 | 0.0004480 | 0.97 | 52.02433 | 41.41099 | 28345282 | 0.226584 | 0.0025512 | 41080455 | 99.99452 | 100 | 30623541 | 88.47 | 43164946 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEULL933JXY | 110585326 | 143995298 | 143995298 | 110585326 | 100 | 55288588 | 0.0000544 | 0.99 | 55.48995 | 40.87436 | 29430905 | 0.252399 | 0.0018215 | 33409972 | 99.99263 | 100 | 32283777 | 89.42 | 50400099 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUMA002VLD | 135552971 | 169095441 | 169095441 | 135552971 | 100 | 67772754 | 0.0000385 | 0.98 | 53.41844 | 46.03283 | 38922106 | 0.310142 | 0.0020246 | 33542470 | 99.99449 | 100 | 41089506 | 91.08 | 62765223 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUMF089KLV | 117156561 | 165059662 | 165059662 | 117156561 | 100 | 58566711 | 0.0001651 | 0.98 | 44.88286 | 38.14853 | 31490598 | 0.341550 | 0.0020028 | 47903101 | 99.98025 | 100 | 35167692 | 85.93 | 52245074 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUML507PFJ | 112923055 | 150315261 | 150315261 | 112923055 | 100 | 56449107 | 0.0001161 | 1.02 | 43.60568 | 44.67974 | 33588188 | 0.396560 | 0.0020184 | 37392206 | 99.97800 | 100 | 37457697 | 87.15 | 51219941 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUMN061ATZ | 93524847 | 128173953 | 128173953 | 93524847 | 100 | 46759563 | 0.0001344 | 0.99 | 57.80673 | 45.27378 | 29016282 | 0.175560 | 0.0027322 | 34649106 | 99.99388 | 100 | 29752572 | 90.24 | 43033290 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUMT184NWC | 136862206 | 224271425 | 224271425 | 136862206 | 100 | 68422512 | 0.0025125 | 0.99 | 39.43972 | 32.22339 | 36139122 | 0.321582 | 0.0021129 | 87409219 | 99.98745 | 100 | 41155454 | 82.33 | 58323568 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUNC876ZB2 | 118137032 | 152219678 | 152219678 | 118137032 | 100 | 59063901 | 0.0001150 | 1.00 | 52.67947 | 45.68107 | 34770809 | 0.295167 | 0.0018412 | 34082646 | 99.99219 | 100 | 38077080 | 88.79 | 53739361 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUNN472ACB | 115095631 | 163191184 | 163191184 | 115095631 | 100 | 57541164 | 0.0002525 | 1.01 | 45.84206 | 40.27677 | 32868036 | 0.322258 | 0.0022235 | 48095553 | 99.98844 | 100 | 37297185 | 86.51 | 50810753 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUNW343RXP | 81656013 | 101975419 | 101975419 | 81656013 | 100 | 40825164 | 0.0000734 | 0.99 | 63.94251 | 45.41374 | 23157025 | 0.172710 | 0.0026231 | 20319406 | 99.99304 | 100 | 24466778 | 91.80 | 38038971 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUPH301NNX | 97626796 | 124778743 | 124778743 | 97626796 | 100 | 48810411 | 0.0007084 | 0.98 | 62.90073 | 38.68959 | 24139662 | 0.168067 | 0.0026556 | 27151947 | 99.99388 | 100 | 25335234 | 91.23 | 45245936 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUPL878MTL | 119315528 | 145479308 | 145479308 | 119315528 | 100 | 59652672 | 0.0001063 | 1.01 | 59.15472 | 45.27052 | 32932752 | 0.255547 | 0.0018693 | 26163780 | 99.99146 | 100 | 35298095 | 91.07 | 55420022 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUPW536ZKZ | 140584593 | 183287662 | 183287662 | 140584593 | 100 | 70282990 | 0.0000454 | 1.00 | 47.46122 | 45.68001 | 41869158 | 0.357446 | 0.0019376 | 42703069 | 99.98676 | 100 | 47060687 | 88.27 | 63578832 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEURJ861MMD | 126644009 | 177617449 | 177617449 | 126644009 | 100 | 63318324 | 0.0001233 | 0.99 | 54.49429 | 33.77473 | 29996606 | 0.204296 | 0.0026134 | 50973440 | 99.99419 | 100 | 32347065 | 88.58 | 57183408 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEURV546WMW | 157220261 | 202295873 | 202295873 | 157220261 | 100 | 78604322 | 0.0002336 | 1.01 | 53.00219 | 40.20670 | 40671295 | 0.293329 | 0.0021206 | 45075612 | 99.99261 | 100 | 42355896 | 90.81 | 72498559 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUUV825HYF | 83800552 | 107396217 | 107396217 | 83800552 | 100 | 41897686 | 0.0004498 | 0.96 | 63.56130 | 37.26202 | 20010218 | 0.157226 | 0.0026666 | 23595665 | 99.99382 | 100 | 20854070 | 91.47 | 38901768 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUVZ050YX7 | 92660498 | 126950374 | 126950374 | 92660498 | 100 | 46327705 | 0.0003695 | 0.96 | 58.44763 | 35.38709 | 22463170 | 0.166282 | 0.0026063 | 34289876 | 99.99451 | 100 | 23548444 | 89.93 | 42302176 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUWN092BVG | 124441297 | 267096673 | 267096673 | 124441297 | 100 | 62217948 | 0.0007366 | 1.02 | 26.44413 | 22.36445 | 29868384 | 0.399273 | 0.0018759 | 142655376 | 99.99566 | 100 | 35643330 | 77.13 | 49313107 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUWT164JRQ | 135918939 | 165861184 | 165861184 | 135918939 | 100 | 67954059 | 0.0006845 | 0.99 | 60.66825 | 36.63712 | 30385906 | 0.236310 | 0.0021812 | 29942245 | 99.99204 | 100 | 31316871 | 92.30 | 63842878 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUXC258VTR | 152107663 | 209900868 | 209900868 | 152107663 | 100 | 76050099 | 0.0001636 | 1.00 | 47.44388 | 37.26139 | 39107873 | 0.318962 | 0.0022160 | 57793205 | 99.99509 | 100 | 42315109 | 88.66 | 68669786 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUXP955XW7 | 114681956 | 149912733 | 149912733 | 114681956 | 100 | 57335068 | 0.0001184 | 1.01 | 52.71462 | 39.41866 | 29550314 | 0.283886 | 0.0018471 | 35230777 | 99.98969 | 100 | 32850947 | 88.44 | 51944509 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUXW311EFC | 104639552 | 288942845 | 288942845 | 104639552 | 100 | 52317273 | 0.0001632 | 1.02 | 18.01321 | 13.99294 | 20216523 | 0.464670 | 0.0020450 | 184303293 | 99.99522 | 100 | 25421145 | 69.72 | 37720814 | NA | NA | NA | NA | NA | NA |
| AnswerALS | CTRL_NEUYM205MRL | 107448896 | 130702708 | 130702708 | 107448896 | 100 | 53721197 | 0.0001384 | 0.98 | 66.54306 | 44.21693 | 28898107 | 0.163942 | 0.0026897 | 23253812 | 99.99395 | 100 | 30061334 | 92.29 | 50334794 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072001A02 | 135941676 | 230048169 | 230048169 | 135941676 | 100 | 67891519 | 0.0000486 | 1.00 | 38.23806 | NA | NA | 0.322099 | 0.0044128 | 94106493 | 99.88330 | NA | NA | 85.10 | 59399312 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072001B02 | 94178800 | 113979200 | 113979200 | 94178800 | 100 | 47033246 | 0.0002407 | 1.04 | 58.12804 | NA | NA | 0.270977 | 0.0041548 | 19800400 | 99.88075 | NA | NA | 91.78 | 44306370 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072002A02 | 128354706 | 233021285 | 233021285 | 128354706 | 100 | 64131194 | 0.0000189 | 1.05 | 32.35120 | NA | NA | 0.385579 | 0.0035951 | 104666579 | 99.92808 | NA | NA | 81.85 | 54374177 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072002B02 | 121345546 | 178706446 | 178706446 | 121345546 | 100 | 60617500 | 0.0000132 | 1.03 | 43.85413 | NA | NA | 0.325116 | 0.0033535 | 57360900 | 99.90890 | NA | NA | 83.17 | 54504534 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072006A01 | 127718938 | 173144213 | 173144213 | 127718938 | 100 | 63815376 | 0.0001075 | 1.08 | 48.64651 | NA | NA | 0.314414 | 0.0034966 | 45425275 | 99.93095 | NA | NA | 89.19 | 58172615 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072006B01 | 126436139 | 163172628 | 163172628 | 126436139 | 100 | 63166742 | 0.0000985 | 1.04 | 52.35554 | NA | NA | 0.298745 | 0.0032790 | 36736489 | 99.91881 | NA | NA | 89.75 | 58149679 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072007A01 | 125824321 | 159464428 | 159464428 | 125824321 | 100 | 62865712 | 0.0000072 | 1.09 | 52.17988 | NA | NA | 0.313698 | 0.0036019 | 33640107 | 99.92617 | NA | NA | 90.13 | 58022536 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072007B01 | 140248486 | 185851687 | 185851687 | 140248486 | 100 | 70064449 | 0.0000110 | 1.02 | 49.51831 | NA | NA | 0.317949 | 0.0033093 | 45603201 | 99.91473 | NA | NA | 88.78 | 64085726 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072008A02 | 113439206 | 174996013 | 174996013 | 113439206 | 100 | 56644047 | 0.0001302 | 1.00 | 44.07174 | NA | NA | 0.287272 | 0.0049033 | 61556807 | 99.86679 | NA | NA | 86.51 | 50470377 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072008B02 | 130419423 | 186533158 | 186533158 | 130419423 | 100 | 65118457 | 0.0001133 | 1.02 | 48.09248 | NA | NA | 0.282421 | 0.0047360 | 56113735 | 99.86006 | NA | NA | 88.34 | 59327132 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072010A02 | 97616064 | 123704269 | 123704269 | 97616064 | 100 | 48751803 | 0.0002113 | 1.02 | 56.76044 | NA | NA | 0.253716 | 0.0043931 | 26088205 | 99.88480 | NA | NA | 90.40 | 45386503 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072010B02 | 97718802 | 128795458 | 128795458 | 97718802 | 100 | 48795660 | 0.0002677 | 1.02 | 53.05946 | NA | NA | 0.271663 | 0.0043221 | 31076656 | 99.86954 | NA | NA | 89.62 | 45162304 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072012A01 | 148024478 | 221266815 | 221266815 | 148024478 | 100 | 73944529 | 0.0000147 | 1.06 | 41.98420 | NA | NA | 0.345136 | 0.0035806 | 73242337 | 99.90852 | NA | NA | 85.59 | 65569118 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072012B01 | 122573980 | 213140649 | 213140649 | 122573980 | 100 | 61231109 | 0.0000237 | 1.09 | 34.86024 | NA | NA | 0.363857 | 0.0034863 | 90566669 | 99.90882 | NA | NA | 82.91 | 52372164 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072013A02 | 118696846 | 192328501 | 192328501 | 118696846 | 100 | 59305314 | 0.0000342 | 1.07 | 38.34418 | NA | NA | 0.350213 | 0.0035889 | 73631655 | 99.92736 | NA | NA | 85.32 | 51716157 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072013B02 | 46670716 | 59683321 | 59683321 | 46670716 | 100 | 23314228 | 0.0000345 | 1.02 | 56.50135 | NA | NA | 0.246293 | 0.0037340 | 13012605 | 99.90945 | NA | NA | 90.82 | 21658777 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072014A02 | 126791091 | 241860665 | 241860665 | 126791091 | 100 | 63323993 | 0.0000448 | 0.97 | 32.89437 | NA | NA | 0.338306 | 0.0042676 | 115069574 | 99.88713 | NA | NA | 82.07 | 53450807 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072014B02 | 128538219 | 181437080 | 181437080 | 128538219 | 100 | 64204227 | 0.0000319 | 1.02 | 48.77057 | NA | NA | 0.282723 | 0.0038709 | 52898861 | 99.89905 | NA | NA | 89.19 | 58677514 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072015A01 | 115356666 | 158112293 | 158112293 | 115356666 | 100 | 57615661 | 0.0001570 | 1.04 | 48.97028 | NA | NA | 0.300918 | 0.0039417 | 42755627 | 99.89134 | NA | NA | 88.68 | 52283322 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072015B01 | 126695445 | 219773032 | 219773032 | 126695445 | 100 | 63292889 | 0.0006390 | 1.05 | 35.27499 | NA | NA | 0.357848 | 0.0034305 | 93077587 | 99.91344 | NA | NA | 83.83 | 54369447 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072018A02 | 111320345 | 138933136 | 138933136 | 111320345 | 100 | 55562883 | 0.0001702 | 1.06 | 54.60476 | NA | NA | 0.291659 | 0.0040284 | 27612791 | 99.82521 | NA | NA | 88.21 | 51515998 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072018B02 | 132755451 | 180480035 | 180480035 | 132755451 | 100 | 66288152 | 0.0001320 | 1.01 | 49.23297 | NA | NA | 0.304696 | 0.0040931 | 47724584 | 99.86505 | NA | NA | 88.72 | 60940845 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072019A02 | 124986603 | 236421103 | 236421103 | 124986603 | 100 | 62440538 | 0.0001764 | 1.02 | 32.79879 | NA | NA | 0.347422 | 0.0038855 | 111434500 | 99.91557 | NA | NA | 82.54 | 52805605 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072019B02 | 147282515 | 183896260 | 183896260 | 147282515 | 100 | 73550040 | 0.0001682 | 0.98 | 53.82492 | NA | NA | 0.303372 | 0.0040621 | 36613745 | 99.87613 | NA | NA | 90.94 | 68691397 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072028A01 | 132870476 | 220521382 | 220521382 | 132870476 | 100 | 66373545 | 0.0001004 | 1.07 | 37.28181 | NA | NA | 0.351354 | 0.0036057 | 87650906 | 99.90714 | NA | NA | 82.84 | 57550940 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072028B01 | 128995074 | 193530490 | 193530490 | 128995074 | 100 | 64452299 | 0.0001071 | 1.06 | 41.89889 | NA | NA | 0.343485 | 0.0031821 | 64535416 | 99.92986 | NA | NA | 85.95 | 57436868 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072029A01 | 106521084 | 182347069 | 182347069 | 106521084 | 100 | 53202122 | 0.0003117 | 1.06 | 36.33133 | NA | NA | 0.346029 | 0.0039574 | 75825985 | 99.89031 | NA | NA | 83.28 | 45652536 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072029B01 | 129663114 | 155124570 | 155124570 | 129663114 | 100 | 64781383 | 0.0000279 | 1.10 | 55.16994 | NA | NA | 0.316344 | 0.0031647 | 25461456 | 99.92261 | NA | NA | 90.69 | 60478486 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072034A01 | 126821822 | 169942398 | 169942398 | 126821822 | 100 | 63361107 | 0.0000734 | 1.05 | 49.69402 | NA | NA | 0.307243 | 0.0036640 | 43120576 | 99.92146 | NA | NA | 88.71 | 58025659 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | 00072034C01 | 136723117 | 187549403 | 187549403 | 136723117 | 100 | 68306236 | 0.0001140 | 1.04 | 45.57472 | NA | NA | 0.349683 | 0.0032756 | 50826286 | 99.91907 | NA | NA | 87.16 | 62019587 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-00iCTR-003 | 72933637 | 115482294 | 115482294 | 72933637 | 100 | 36430618 | 0.0000614 | 1.03 | 48.36477 | NA | NA | 0.196205 | 0.0021612 | 42548657 | 99.90073 | NA | NA | 86.39 | 32117381 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-00iCTR-004 | 80664165 | 114902116 | 114902116 | 80664165 | 100 | 40291268 | 0.0000522 | 1.06 | 53.36115 | NA | NA | 0.205768 | 0.0019302 | 34237951 | 99.89880 | NA | NA | 87.58 | 36178657 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-25iCTR-003 | 90791001 | 196170471 | 196170471 | 90791001 | 100 | 45356754 | 0.0001678 | 1.04 | 29.61257 | NA | NA | 0.321581 | 0.0020212 | 105379470 | 99.91465 | NA | NA | 76.83 | 35959903 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-25iCTR-004 | 105034279 | 152195347 | 152195347 | 105034279 | 100 | 52463612 | 0.0000295 | 1.08 | 50.06550 | NA | NA | 0.243061 | 0.0017331 | 47161068 | 99.89808 | NA | NA | 85.75 | 46397163 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-28iALS-003 | 60575786 | 85175631 | 85175631 | 60575786 | 100 | 30261072 | 0.0000304 | 1.00 | 56.65664 | NA | NA | 0.169235 | 0.0019201 | 24599845 | 99.91145 | NA | NA | 89.22 | 27509794 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-28iALS-005 | 85676346 | 138127203 | 138127203 | 85676346 | 100 | 42771822 | 0.0000311 | 1.02 | 46.50457 | NA | NA | 0.215862 | 0.0017702 | 52450857 | 99.84511 | NA | NA | 85.96 | 37588074 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-29iALS-003 | 87345844 | 104514733 | 104514733 | 87345844 | 100 | 43633538 | 0.0000234 | 1.03 | 62.47783 | NA | NA | 0.228698 | 0.0018449 | 17168889 | 99.90982 | NA | NA | 90.52 | 40374838 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-29iALS-004 | 95816596 | 141144444 | 141144444 | 95816596 | 100 | 47865904 | 0.0000585 | 1.05 | 48.69636 | NA | NA | 0.251449 | 0.0017006 | 45327848 | 99.91151 | NA | NA | 86.92 | 42550998 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-30iALS-003 | 77416918 | 102396365 | 102396365 | 77416918 | 100 | 38671139 | 0.0000805 | 1.04 | 58.61526 | NA | NA | 0.194683 | 0.0019603 | 24979447 | 99.90359 | NA | NA | 88.96 | 35212928 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-30iALS-004 | 102751248 | 136491201 | 136491201 | 102751248 | 100 | 51326745 | 0.0000490 | 1.07 | 58.26979 | NA | NA | 0.197065 | 0.0017537 | 33739953 | 99.90486 | NA | NA | 89.08 | 46825808 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-52iALS-003 | 73314114 | 105152444 | 105152444 | 73314114 | 100 | 36626533 | 0.0000241 | 1.02 | 49.57568 | NA | NA | 0.256968 | 0.0018323 | 31838330 | 99.91673 | NA | NA | 87.63 | 32786448 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-52iALS-004 | 95698993 | 133431493 | 133431493 | 95698993 | 100 | 47804764 | 0.0000155 | 1.07 | 50.82951 | NA | NA | 0.262022 | 0.0016450 | 37732500 | 99.90651 | NA | NA | 87.51 | 43059847 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-83iCTR-003 | 95760241 | 243258163 | 243258163 | 95760241 | 100 | 47840562 | 0.0000123 | 1.08 | 22.95447 | NA | NA | 0.376408 | 0.0020284 | 147497922 | 99.91738 | NA | NA | 71.68 | 35437258 | NA | NA | NA | NA | NA | NA |
| neurolincs.diMN | A-042-83iCTR-004 | 84808205 | 166729922 | 166729922 | 84808205 | 100 | 42367425 | 0.0000080 | 1.09 | 33.60215 | NA | NA | 0.301175 | 0.0017554 | 81921717 | 99.91350 | NA | NA | 79.32 | 34527944 | NA | NA | NA | NA | NA | NA |
| catanese | c9orf72_1 | 75957394 | 81967185 | 81967185 | 75957394 | 100 | 37968138 | 0.0000180 | 1.08 | 61.65157 | NA | NA | 0.315076 | 0.0025560 | 6009791 | 99.97220 | NA | NA | 95.02 | 36788530 | NA | NA | NA | NA | NA | NA |
| catanese | c9orf72_2 | 72919132 | 78480260 | 78480260 | 72919132 | 100 | 36451110 | 0.0000282 | 1.05 | 62.35228 | NA | NA | 0.309170 | 0.0026208 | 5561128 | 99.97681 | NA | NA | 95.08 | 35311214 | NA | NA | NA | NA | NA | NA |
| catanese | c9orf72_3 | 76337728 | 82563723 | 82563723 | 76337728 | 100 | 38161015 | 0.0000060 | 1.06 | 58.64808 | NA | NA | 0.346512 | 0.0027519 | 6225995 | 99.97944 | NA | NA | 94.71 | 36947989 | NA | NA | NA | NA | NA | NA |
| catanese | c9orf72_4 | 71229641 | 76888537 | 76888537 | 71229641 | 100 | 35607323 | 0.0000226 | 1.10 | 60.84190 | NA | NA | 0.323337 | 0.0025268 | 5658896 | 99.97895 | NA | NA | 94.78 | 34466646 | NA | NA | NA | NA | NA | NA |
| catanese | c9orf72_5 | 70109568 | 76105593 | 76105593 | 70109568 | 100 | 35046568 | 0.0000163 | 1.09 | 56.96976 | NA | NA | 0.362158 | 0.0026023 | 5996025 | 99.97656 | NA | NA | 94.61 | 33883013 | NA | NA | NA | NA | NA | NA |
| catanese | c9orf72_6 | 69814167 | 75301066 | 75301066 | 69814167 | 100 | 34898923 | 0.0000098 | 1.11 | 57.44992 | NA | NA | 0.361781 | 0.0026903 | 5486899 | 99.97662 | NA | NA | 94.95 | 33801000 | NA | NA | NA | NA | NA | NA |
| catanese | ctrl_1 | 65434941 | 70580531 | 70580531 | 65434941 | 100 | 32708636 | 0.0000245 | 1.08 | 59.90526 | NA | NA | 0.334629 | 0.0025768 | 5145590 | 99.97300 | NA | NA | 95.09 | 31699462 | NA | NA | NA | NA | NA | NA |
| catanese | ctrl_2 | 60047749 | 64571298 | 64571298 | 60047749 | 100 | 30017201 | 0.0000076 | 1.06 | 62.14138 | NA | NA | 0.312248 | 0.0023685 | 4523549 | 99.97777 | NA | NA | 95.42 | 29103408 | NA | NA | NA | NA | NA | NA |
| catanese | ctrl_3 | 63620482 | 68216444 | 68216444 | 63620482 | 100 | 31804721 | 0.0000107 | 1.08 | 59.72607 | NA | NA | 0.341274 | 0.0024669 | 4595962 | 99.98265 | NA | NA | 95.50 | 30862009 | NA | NA | NA | NA | NA | NA |
| catanese | fus_1 | 67955571 | 73428734 | 73428734 | 67955571 | 100 | 33970617 | 0.0000100 | 1.06 | 60.63928 | NA | NA | 0.325379 | 0.0025217 | 5473163 | 99.97890 | NA | NA | 95.00 | 32894443 | NA | NA | NA | NA | NA | NA |
| catanese | fus_2 | 63220005 | 68675328 | 68675328 | 63220005 | 100 | 31603980 | 0.0000072 | 1.07 | 60.85049 | NA | NA | 0.319067 | 0.0025170 | 5455323 | 99.98095 | NA | NA | 95.21 | 30591145 | NA | NA | NA | NA | NA | NA |
| catanese | fus_3 | 74148845 | 79882326 | 79882326 | 74148845 | 100 | 37066760 | 0.0000092 | 1.05 | 57.39093 | NA | NA | 0.363480 | 0.0025698 | 5733481 | 99.97933 | NA | NA | 95.30 | 35918835 | NA | NA | NA | NA | NA | NA |
| catanese | fus_4 | 59851095 | 64881696 | 64881696 | 59851095 | 100 | 29921067 | 0.0000190 | 1.07 | 61.06491 | NA | NA | 0.318017 | 0.0025564 | 5030601 | 99.98503 | NA | NA | 95.41 | 28970978 | NA | NA | NA | NA | NA | NA |
| catanese | fus_5 | 70100137 | 75733720 | 75733720 | 70100137 | 100 | 35043505 | 0.0000162 | 1.06 | 55.75257 | NA | NA | 0.379645 | 0.0024940 | 5633583 | 99.98127 | NA | NA | 95.09 | 33946048 | NA | NA | NA | NA | NA | NA |
| catanese | fus_6 | 66401477 | 72139932 | 72139932 | 66401477 | 100 | 33195335 | 0.0000102 | 1.08 | 58.00465 | NA | NA | 0.350565 | 0.0025423 | 5738455 | 99.98372 | NA | NA | 94.95 | 32122277 | NA | NA | NA | NA | NA | NA |
| catanese | iso_1 | 65420693 | 70669639 | 70669639 | 65420693 | 100 | 32703372 | 0.0000000 | 1.06 | 60.57990 | NA | NA | 0.326263 | 0.0027316 | 5248946 | 99.97868 | NA | NA | 95.13 | 31687063 | NA | NA | NA | NA | NA | NA |
| catanese | iso_2 | 72233630 | 78605662 | 78605662 | 72233630 | 100 | 36107695 | 0.0000000 | 1.05 | 58.27189 | NA | NA | 0.346863 | 0.0024793 | 6372032 | 99.97475 | NA | NA | 95.10 | 34960517 | NA | NA | NA | NA | NA | NA |
| catanese | iso_3 | 70716047 | 76451317 | 76451317 | 70716047 | 100 | 35350396 | 0.0000065 | 1.04 | 61.47153 | NA | NA | 0.316114 | 0.0024646 | 5735270 | 99.97843 | NA | NA | 95.15 | 34278261 | NA | NA | NA | NA | NA | NA |
| dafinca | c9orf72_1 | 121035567 | 132747772 | 132747772 | 121035567 | 100 | 60511122 | 0.0000018 | 1.19 | 58.86387 | NA | NA | 0.331559 | 0.0026354 | 11712205 | 99.98899 | NA | NA | 92.58 | 57798843 | NA | NA | NA | NA | NA | NA |
| dafinca | c9orf72_2 | 118789660 | 132869385 | 132869385 | 118789660 | 100 | 59388555 | 0.0000038 | 1.31 | 65.47521 | NA | NA | 0.238722 | 0.0023471 | 14079725 | 99.98944 | NA | NA | 91.76 | 56299561 | NA | NA | NA | NA | NA | NA |
| dafinca | c9orf72_3 | 101537136 | 109650109 | 109650109 | 101537136 | 100 | 50761452 | 0.0000000 | 1.14 | 65.64582 | NA | NA | 0.265317 | 0.0024822 | 8112973 | 99.98598 | NA | NA | 91.22 | 48515807 | NA | NA | NA | NA | NA | NA |
| dafinca | c9orf72_4 | 106049359 | 119503299 | 119503299 | 106049359 | 100 | 53018709 | 0.0000000 | 1.21 | 62.38078 | NA | NA | 0.269820 | 0.0024909 | 13453940 | 99.98874 | NA | NA | 92.11 | 50254110 | NA | NA | NA | NA | NA | NA |
| dafinca | ctrl_1 | 105491420 | 119502002 | 119502002 | 105491420 | 100 | 52737233 | 0.0000021 | 1.22 | 67.63313 | NA | NA | 0.203468 | 0.0027350 | 14010582 | 99.98393 | NA | NA | 91.40 | 50043374 | NA | NA | NA | NA | NA | NA |
| dafinca | iso_1 | 110514258 | 126081076 | 126081076 | 110514258 | 100 | 55250944 | 0.0000020 | 1.14 | 58.38462 | NA | NA | 0.305962 | 0.0025204 | 15566818 | 99.98881 | NA | NA | 89.66 | 51904662 | NA | NA | NA | NA | NA | NA |
| dafinca | iso_2 | 106736217 | 117587500 | 117587500 | 106736217 | 100 | 53359671 | 0.0000000 | 1.16 | 59.85868 | NA | NA | 0.315709 | 0.0026161 | 10851283 | 99.98419 | NA | NA | 90.48 | 50824778 | NA | NA | NA | NA | NA | NA |
| dafinca | iso_3 | 106149403 | 119518192 | 119518192 | 106149403 | 100 | 53067334 | 0.0000063 | 1.19 | 67.64927 | NA | NA | 0.208851 | 0.0026364 | 13368789 | 99.98612 | NA | NA | 90.97 | 50439866 | NA | NA | NA | NA | NA | NA |
| dafinca | iso_4 | 92324252 | 103350221 | 103350221 | 92324252 | 100 | 46155034 | 0.0000000 | 1.18 | 57.64835 | NA | NA | 0.329921 | 0.0026080 | 11025969 | 99.98464 | NA | NA | 89.83 | 43738930 | NA | NA | NA | NA | NA | NA |
| dafinca | iso_5 | 110135429 | 123636396 | 123636396 | 110135429 | 100 | 55060726 | 0.0000000 | 1.07 | 50.65312 | NA | NA | 0.408146 | 0.0024266 | 13500967 | 99.98731 | NA | NA | 89.57 | 51988008 | NA | NA | NA | NA | NA | NA |
| dafinca | iso_6 | 112546857 | 126042797 | 126042797 | 112546857 | 100 | 56265174 | 0.0000000 | 1.23 | 45.18061 | NA | NA | 0.474039 | 0.0025985 | 13495940 | 99.98533 | NA | NA | 89.66 | 53279237 | NA | NA | NA | NA | NA | NA |
| dafinca | iso_7 | 94610729 | 105135911 | 105135911 | 94610729 | 100 | 47299602 | 0.0000024 | 1.23 | 59.79154 | NA | NA | 0.310400 | 0.0024351 | 10525182 | 99.98782 | NA | NA | 90.88 | 44856979 | NA | NA | NA | NA | NA | NA |
| dafinca | ctrl_1 | 16576302 | 17489968 | 17489968 | 16576302 | 100 | 8275371 | 0.0000000 | 1.08 | 85.36618 | NA | NA | 0.073477 | 0.0041740 | 913666 | 99.84580 | NA | NA | 96.02 | 8070745 | NA | NA | NA | NA | NA | NA |
| dafinca | ctrl_2 | 18972276 | 20097878 | 20097878 | 18972276 | 100 | 9472448 | 0.0000000 | 1.09 | 83.99444 | NA | NA | 0.082375 | 0.0040685 | 1125602 | 99.85568 | NA | NA | 95.60 | 9202716 | NA | NA | NA | NA | NA | NA |
| dafinca | ctrl_3 | 19783273 | 20867596 | 20867596 | 19783273 | 100 | 9878007 | 0.0000000 | 1.11 | 84.84853 | NA | NA | 0.079675 | 0.0039749 | 1084323 | 99.86221 | NA | NA | 96.04 | 9633247 | NA | NA | NA | NA | NA | NA |
| dafinca | ctrl_4 | 15583580 | 16625552 | 16625552 | 15583580 | 100 | 7776614 | 0.0000000 | 1.21 | 81.17492 | NA | NA | 0.106605 | 0.0039203 | 1041972 | 99.80523 | NA | NA | 91.17 | 7568676 | NA | NA | NA | NA | NA | NA |
| dafinca | tardbp_1 | 19574454 | 20693487 | 20693487 | 19574454 | 100 | 9772054 | 0.0000000 | 1.21 | 83.90709 | NA | NA | 0.086220 | 0.0038139 | 1119033 | 99.84497 | NA | NA | 94.26 | 9511682 | NA | NA | NA | NA | NA | NA |
| dafinca | tardbp_2 | 18517769 | 19719622 | 19719622 | 18517769 | 100 | 9239181 | 0.0000372 | 1.23 | 82.91080 | NA | NA | 0.089737 | 0.0041516 | 1201853 | 99.78719 | NA | NA | 93.02 | 8998264 | NA | NA | NA | NA | NA | NA |
| dafinca | tardbp_3 | 20485715 | 21679042 | 21679042 | 20485715 | 100 | 10224310 | 0.0000000 | 1.19 | 81.68852 | NA | NA | 0.109326 | 0.0039982 | 1193327 | 99.81892 | NA | NA | 93.58 | 9957003 | NA | NA | NA | NA | NA | NA |
| dafinca | tardbp_4 | 21895246 | 23787368 | 23787368 | 21895246 | 100 | 10932302 | 0.0000211 | 1.29 | 71.93412 | NA | NA | 0.191469 | 0.0039524 | 1892122 | 99.86005 | NA | NA | 93.74 | 10582849 | NA | NA | NA | NA | NA | NA |
| dafinca | tardbp_5 | 18544776 | 19538517 | 19538517 | 18544776 | 100 | 9258793 | 0.0000129 | 1.09 | 84.43084 | NA | NA | 0.083507 | 0.0040231 | 993741 | 99.85338 | NA | NA | 95.57 | 9003671 | NA | NA | NA | NA | NA | NA |
| dafinca | tardbp_6 | 20071514 | 21044889 | 21044889 | 20071514 | 100 | 10025089 | 0.0000118 | 1.09 | 85.35948 | NA | NA | 0.080760 | 0.0036381 | 973375 | 99.89370 | NA | NA | 96.13 | 9778365 | NA | NA | NA | NA | NA | NA |
| luisier | d35_ctrl_1 | 14137164 | 17365755 | 17365755 | 14137164 | 100 | 14137164 | 0.0000319 | 0.97 | NA | NA | NA | 0.424189 | 0.0025543 | 3228591 | 0.00000 | NA | NA | 89.92 | 12777849 | 1.9300484 | NA | 47 | 60.00000 | 35.22582 | 47 |
| luisier | d35_ctrl_2 | 12395390 | 15087201 | 15087201 | 12395390 | 100 | 12395390 | 0.0000000 | 0.92 | NA | NA | NA | 0.435478 | 0.0028154 | 2691811 | 0.00000 | NA | NA | 90.20 | 11235044 | 1.9136214 | NA | 47 | 60.00000 | 36.35613 | 47 |
| luisier | d35_ctrl_3 | 13781703 | 16430800 | 16430800 | 13781703 | 100 | 13781703 | 0.0000000 | 0.92 | NA | NA | NA | 0.455100 | 0.0027615 | 2649097 | 0.00000 | NA | NA | 90.76 | 12561469 | 1.8540827 | NA | 47 | 60.00000 | 37.38918 | 47 |
| luisier | d35_vcp_1 | 10394568 | 12882428 | 12882428 | 10394568 | 100 | 10394568 | 0.0000135 | 1.09 | NA | NA | NA | 0.446962 | 0.0024339 | 2487860 | 0.00000 | NA | NA | 89.00 | 9302422 | 2.0395963 | NA | 48 | 60.00000 | 37.34052 | 48 |
| luisier | d35_vcp_2 | 15815865 | 19279401 | 19279401 | 15815865 | 100 | 15815865 | 0.0000000 | 1.00 | NA | NA | NA | 0.443607 | 0.0024008 | 3463536 | 0.00000 | NA | NA | 90.36 | 14356502 | 2.0067293 | NA | 48 | 60.00000 | 36.71011 | 48 |
| luisier | d35_vcp_3 | 5906382 | 7352632 | 7352632 | 5906382 | 100 | 5906382 | 0.0000000 | 0.87 | NA | NA | NA | 0.282392 | 0.0029136 | 1446250 | 0.00000 | NA | NA | 90.28 | 5362641 | 1.8340739 | NA | 45 | 60.00000 | 22.58967 | 45 |
| wang | iso_1 | 30043364 | 31484983 | 31484983 | 30043364 | 100 | 14914560 | 0.0000161 | 1.08 | 77.98233 | NA | NA | 0.157261 | 0.0063193 | 1441619 | 99.28688 | NA | NA | 90.82 | 14677818 | NA | NA | NA | NA | NA | NA |
| wang | iso_2 | 30198322 | 31651805 | 31651805 | 30198322 | 100 | 14981698 | 0.0000641 | 1.04 | 78.00677 | NA | NA | 0.156546 | 0.0065433 | 1453483 | 99.22206 | NA | NA | 90.39 | 14766976 | NA | NA | NA | NA | NA | NA |
| wang | sod1_1 | 30809361 | 32337592 | 32337592 | 30809361 | 100 | 15287653 | 0.0000315 | 1.06 | 78.14520 | NA | NA | 0.153305 | 0.0065095 | 1528231 | 99.24031 | NA | NA | 90.32 | 15039892 | NA | NA | NA | NA | NA | NA |
| wang | sod1_2 | 30686515 | 32213431 | 32213431 | 30686515 | 100 | 15236081 | 0.0000159 | 1.05 | 78.11696 | NA | NA | 0.154028 | 0.0062301 | 1526916 | 99.30147 | NA | NA | 90.98 | 14983631 | NA | NA | NA | NA | NA | NA |
| kiskinis | iso_1 | 12452702 | 17772558 | 17772558 | 12452702 | 100 | 6217630 | 0.0000000 | 1.23 | 55.95839 | NA | NA | 0.138765 | 0.0025517 | 5319856 | 99.85993 | NA | NA | 80.22 | 5657335 | NA | NA | NA | NA | NA | NA |
| kiskinis | iso_2 | 10126374 | 14391602 | 14391602 | 10126374 | 100 | 5057244 | 0.0000000 | 1.17 | 59.25709 | NA | NA | 0.092385 | 0.0055493 | 4265228 | 99.88262 | NA | NA | 57.22 | 4604554 | NA | NA | NA | NA | NA | NA |
| kiskinis | iso_3 | 18104053 | 32559601 | 32559601 | 18104053 | 100 | 9040767 | 0.0000000 | 1.21 | 41.11135 | NA | NA | 0.188924 | 0.0029665 | 14455548 | 99.87561 | NA | NA | 72.59 | 7772222 | NA | NA | NA | NA | NA | NA |
| kiskinis | sod1_1 | 16718799 | 18243146 | 18243146 | 16718799 | 100 | 8343800 | 0.0000747 | 1.11 | 36.75684 | NA | NA | 0.579065 | 0.0036592 | 1524347 | 99.81339 | NA | NA | 71.79 | 8048144 | NA | NA | NA | NA | NA | NA |
| kiskinis | sod1_2 | 30656110 | 32740754 | 32740754 | 30656110 | 100 | 15295018 | 0.0000000 | 1.15 | 39.27142 | NA | NA | 0.563443 | 0.0020756 | 2084644 | 99.78447 | NA | NA | 91.61 | 14850599 | NA | NA | NA | NA | NA | NA |
| sareen | c9orf72_1 | 24845406 | 33212470 | 33212470 | 24845406 | 100 | 24845406 | 0.0000101 | 1.09 | NA | NA | NA | 0.493514 | 0.0028375 | 8367064 | 0.00000 | NA | NA | 86.58 | 21655725 | 1.7767771 | NA | 50 | 50.00000 | 42.08267 | 50 |
| sareen | c9orf72_2 | 28151852 | 37739985 | 37739985 | 28151852 | 100 | 28151852 | 0.0000000 | 1.10 | NA | NA | NA | 0.513295 | 0.0028173 | 9588133 | 0.00000 | NA | NA | 86.21 | 24431401 | 1.9300992 | NA | 50 | 50.00000 | 43.94880 | 50 |
| sareen | c9orf72_3 | 41219527 | 56126483 | 56126483 | 41219527 | 100 | 41219527 | 0.0000099 | 1.07 | NA | NA | NA | 0.527217 | 0.0030292 | 14906956 | 0.00000 | NA | NA | 86.16 | 35777527 | 1.7798850 | NA | 50 | 50.00000 | 45.31533 | 50 |
| sareen | c9orf72_4 | 36409834 | 51259702 | 51259702 | 36409834 | 100 | 36409834 | 0.0000035 | 1.09 | NA | NA | NA | 0.556295 | 0.0027945 | 14849868 | 0.00000 | NA | NA | 85.25 | 31216316 | 1.7837984 | NA | 49 | 50.00000 | 48.03861 | 50 |
| sareen | ctrl_1 | 34637930 | 47037378 | 47037378 | 34637930 | 100 | 34637930 | 0.0000113 | 1.09 | NA | NA | NA | 0.515683 | 0.0031012 | 12399448 | 0.00000 | NA | NA | 86.02 | 29995779 | 1.7143701 | NA | 49 | 50.00000 | 44.23380 | 50 |
| sareen | ctrl_2 | 36036948 | 51713786 | 51713786 | 36036948 | 100 | 36036948 | 0.0000040 | 1.07 | NA | NA | NA | 0.529704 | 0.0030175 | 15676838 | 0.00000 | NA | NA | 83.66 | 30377803 | 1.8764297 | NA | 50 | 50.00000 | 45.92756 | 50 |
| sareen | ctrl_3 | 30120447 | 41597088 | 41597088 | 30120447 | 100 | 30120447 | 0.0000000 | 1.10 | NA | NA | NA | 0.527209 | 0.0028863 | 11476641 | 0.00000 | NA | NA | 85.80 | 26005996 | 1.7897096 | NA | 50 | 50.00000 | 45.40106 | 50 |
| sareen | ctrl_4 | 32042851 | 45335936 | 45335936 | 32042851 | 100 | 32042851 | 0.0000000 | 1.11 | NA | NA | NA | 0.564093 | 0.0028951 | 13293085 | 0.00000 | NA | NA | 84.18 | 27146239 | 1.8080937 | NA | 50 | 50.00000 | 49.01965 | 50 |
| sommer | c9orf72_1 | 64336887 | 68180133 | 68180133 | 64336887 | 100 | 32164997 | 0.0000211 | 1.15 | 57.56799 | NA | NA | 0.371038 | 0.0035648 | 3843246 | 99.98929 | NA | NA | 95.53 | 31119676 | NA | NA | NA | NA | NA | NA |
| sommer | c9orf72_2 | 59830017 | 63876868 | 63876868 | 59830017 | 100 | 29911673 | 0.0000151 | 1.18 | 58.66177 | NA | NA | 0.354318 | 0.0044798 | 4046851 | 99.98885 | NA | NA | 95.38 | 28942710 | NA | NA | NA | NA | NA | NA |
| sommer | c9orf72_3 | 69515736 | 74358559 | 74358559 | 69515736 | 100 | 34754477 | 0.0000065 | 1.16 | 53.89325 | NA | NA | 0.405207 | 0.0037721 | 4842823 | 99.99024 | NA | NA | 95.36 | 33598568 | NA | NA | NA | NA | NA | NA |
| sommer | c9orf72_4 | 80391972 | 86053600 | 86053600 | 80391972 | 100 | 40188899 | 0.0000113 | 1.19 | 56.87527 | NA | NA | 0.371822 | 0.0037454 | 5661628 | 99.98237 | NA | NA | 95.13 | 38828950 | NA | NA | NA | NA | NA | NA |
| sommer | c9orf72_5 | 61652359 | 65967842 | 65967842 | 61652359 | 100 | 30821964 | 0.0000074 | 1.16 | 59.42428 | NA | NA | 0.344064 | 0.0033644 | 4315483 | 99.98632 | NA | NA | 95.58 | 29791587 | NA | NA | NA | NA | NA | NA |
| sommer | c9orf72_6 | 70120140 | 75192973 | 75192973 | 70120140 | 100 | 35054981 | 0.0000227 | 1.20 | 59.53601 | NA | NA | 0.340776 | 0.0038008 | 5072833 | 99.98548 | NA | NA | 95.07 | 33842839 | NA | NA | NA | NA | NA | NA |
| sommer | ctrl_1 | 61955188 | 66357819 | 66357819 | 61955188 | 100 | 30973008 | 0.0000256 | 1.15 | 60.87844 | NA | NA | 0.326305 | 0.0055210 | 4402631 | 99.98520 | NA | NA | 94.27 | 29911391 | NA | NA | NA | NA | NA | NA |
| sommer | ctrl_2 | 70169531 | 75521771 | 75521771 | 70169531 | 100 | 35078491 | 0.0000097 | 1.13 | 60.25348 | NA | NA | 0.330383 | 0.0048517 | 5352240 | 99.98212 | NA | NA | 94.38 | 33866702 | NA | NA | NA | NA | NA | NA |
| sommer | ctrl_3 | 62797464 | 67487027 | 67487027 | 62797464 | 100 | 31393786 | 0.0000327 | 1.16 | 61.94428 | NA | NA | 0.312421 | 0.0042264 | 4689563 | 99.98425 | NA | NA | 95.09 | 30310132 | NA | NA | NA | NA | NA | NA |
| sommer | ctrl_4 | 64222789 | 69085377 | 69085377 | 64222789 | 100 | 32105084 | 0.0000282 | 1.22 | 55.42455 | NA | NA | 0.383816 | 0.0037653 | 4862588 | 99.98035 | NA | NA | 95.04 | 30986550 | NA | NA | NA | NA | NA | NA |
| sommer | ctrl_5 | 62956346 | 66994033 | 66994033 | 62956346 | 100 | 31473476 | 0.0000036 | 1.21 | 58.64255 | NA | NA | 0.356663 | 0.0042383 | 4037687 | 99.98508 | NA | NA | 95.39 | 30464986 | NA | NA | NA | NA | NA | NA |
| sommer | ctrl_6 | 61029668 | 64804558 | 64804558 | 61029668 | 100 | 30511929 | 0.0000185 | 1.27 | 55.20029 | NA | NA | 0.396642 | 0.0044914 | 3774890 | 99.99048 | NA | NA | 95.64 | 29601506 | NA | NA | NA | NA | NA | NA |
| sterneckert | c9orf72_1 | 29486569 | 33917688 | 33917688 | 29486569 | 100 | 29486569 | 0.0000120 | 0.90 | NA | NA | NA | 0.579341 | 0.0027601 | 4431119 | 0.00000 | NA | NA | 92.87 | 27517196 | 1.9098705 | NA | 48 | 76.00000 | 47.13294 | 48 |
| sterneckert | c9orf72_2 | 31243868 | 36606014 | 36606014 | 31243868 | 100 | 31243868 | 0.0000038 | 0.93 | NA | NA | NA | 0.577691 | 0.0028034 | 5362146 | 0.00000 | NA | NA | 92.55 | 29058077 | 1.7791890 | NA | 48 | 76.00000 | 46.60611 | 48 |
| sterneckert | c9orf72_3 | 32063553 | 37667089 | 37667089 | 32063553 | 100 | 32063553 | 0.0000148 | 0.94 | NA | NA | NA | 0.588367 | 0.0027117 | 5603536 | 0.00000 | NA | NA | 92.49 | 29798603 | 2.0554790 | NA | 48 | 76.00000 | 47.71547 | 48 |
| sterneckert | ctrl_1 | 33374081 | 38505971 | 38505971 | 33374081 | 100 | 33374081 | 0.0000071 | 0.89 | NA | NA | NA | 0.601435 | 0.0028147 | 5131890 | 0.00000 | NA | NA | 92.91 | 31164000 | 2.0262374 | NA | 47 | 76.00000 | 48.85676 | 48 |
| sterneckert | ctrl_2 | 34261753 | 40216782 | 40216782 | 34261753 | 100 | 34261753 | 0.0000103 | 0.92 | NA | NA | NA | 0.614326 | 0.0027964 | 5955029 | 0.00000 | NA | NA | 92.58 | 31871446 | 1.9240435 | NA | 47 | 76.00000 | 49.77593 | 48 |
| sterneckert | ctrl_3 | 33589817 | 38967746 | 38967746 | 33589817 | 100 | 33589817 | 0.0000140 | 0.91 | NA | NA | NA | 0.610028 | 0.0028401 | 5377929 | 0.00000 | NA | NA | 92.83 | 31330830 | 1.6798903 | NA | 47 | 76.00000 | 49.31932 | 48 |
| kapeli | ctrl_1 | 20435843 | 25667654 | 25667654 | 20435843 | 100 | 20435843 | 0.0000061 | 0.85 | NA | NA | NA | 0.554723 | 0.0047651 | 5231811 | 0.00000 | NA | NA | 87.77 | 18036576 | 2.1085959 | NA | 48 | 50.00000 | 22.71533 | 48 |
| kapeli | ctrl_2 | 30183571 | 37590329 | 37590329 | 30183571 | 100 | 30183571 | 0.0000000 | 0.86 | NA | NA | NA | 0.582816 | 0.0034462 | 7406758 | 0.00000 | NA | NA | 86.97 | 26825417 | 1.6451473 | NA | 47 | 50.00000 | 49.82654 | 47 |
| kapeli | ctrl_3 | 12990116 | 16093163 | 16093163 | 12990116 | 100 | 12990116 | 0.0000000 | 0.83 | NA | NA | NA | 0.455431 | 0.0066942 | 3103047 | 0.00000 | NA | NA | 87.30 | 11590391 | 1.6911131 | NA | 47 | 50.00000 | 36.04786 | 47 |
| kapeli | fus_1 | 11628347 | 14571553 | 14571553 | 11628347 | 100 | 11628347 | 0.0000000 | 0.89 | NA | NA | NA | 0.421617 | 0.0026919 | 2943206 | 0.00000 | NA | NA | 88.79 | 10382274 | 1.6719885 | NA | 47 | 50.00000 | 35.60242 | 47 |
| kapeli | fus_2 | 20542668 | 26014667 | 26014667 | 20542668 | 100 | 20542668 | 0.0000130 | 0.82 | NA | NA | NA | 0.506807 | 0.0025970 | 5471999 | 0.00000 | NA | NA | 88.57 | 18294585 | 1.7357264 | NA | 47 | 50.00000 | 43.59158 | 48 |
| kapeli | fus_3 | 29894560 | 37829682 | 37829682 | 29894560 | 100 | 29894560 | 0.0000089 | 0.82 | NA | NA | NA | 0.567029 | 0.0027094 | 7935122 | 0.00000 | NA | NA | 88.36 | 26553868 | 1.6529225 | NA | 48 | 50.00000 | 48.45148 | 48 |
| desantis | ctrl_1 | 36464752 | 66855277 | 66855277 | 36464752 | 100 | 18210429 | 0.0000810 | 1.04 | 38.58190 | NA | NA | 0.251628 | 0.0022052 | 30390525 | 99.87963 | NA | NA | 82.22 | 15195161 | NA | NA | NA | NA | NA | NA |
| desantis | ctrl_2 | 40806682 | 97439508 | 97439508 | 40806682 | 100 | 20381742 | 0.0001051 | 1.01 | 17.30446 | NA | NA | 0.549032 | 0.0022554 | 56632826 | 99.89414 | NA | NA | 70.47 | 14822076 | NA | NA | NA | NA | NA | NA |
| desantis | ctrl_3 | 39635903 | 75448922 | 75448922 | 39635903 | 100 | 19795267 | 0.0001564 | 1.00 | 36.44447 | NA | NA | 0.265744 | 0.0021035 | 35813019 | 99.88554 | NA | NA | 81.60 | 16465064 | NA | NA | NA | NA | NA | NA |
| desantis | fus_1 | 35612797 | 66471955 | 66471955 | 35612797 | 100 | 17785490 | 0.0000883 | 0.99 | 35.21769 | NA | NA | 0.300553 | 0.0021299 | 30859158 | 99.88258 | NA | NA | 79.99 | 14476588 | NA | NA | NA | NA | NA | NA |
| desantis | fus_2 | 47294523 | 107673051 | 107673051 | 47294523 | 100 | 23619629 | 0.0000349 | 1.02 | 14.42152 | NA | NA | 0.640610 | 0.0022572 | 60378528 | 99.88315 | NA | NA | 72.36 | 17684239 | NA | NA | NA | NA | NA | NA |
| desantis | fus_3 | 37794691 | 71049470 | 71049470 | 37794691 | 100 | 18874586 | 0.0000409 | 1.03 | 35.62457 | NA | NA | 0.289365 | 0.0021430 | 33254779 | 99.87956 | NA | NA | 81.44 | 15659611 | NA | NA | NA | NA | NA | NA |
| smith | ctrl_1 | 56523441 | 63212608 | 63212608 | 56523441 | 100 | 28252066 | 0.0000000 | 1.14 | 76.33318 | NA | NA | 0.101840 | 0.0020922 | 6689167 | 99.96584 | NA | NA | 92.92 | 26581477 | NA | NA | NA | NA | NA | NA |
| smith | ctrl_2 | 72973159 | 81543822 | 81543822 | 72973159 | 100 | 36477011 | 0.0000033 | 1.12 | 75.04343 | NA | NA | 0.119042 | 0.0019577 | 8570663 | 99.97378 | NA | NA | 93.03 | 34320173 | NA | NA | NA | NA | NA | NA |
| smith | tardbp_1 | 81164834 | 89990577 | 89990577 | 81164834 | 100 | 40567587 | 0.0000155 | 1.11 | 78.09236 | NA | NA | 0.091812 | 0.0021474 | 8825743 | 99.96346 | NA | NA | 93.09 | 38444351 | NA | NA | NA | NA | NA | NA |
| smith | tardbp_2 | 81670004 | 90694956 | 90694956 | 81670004 | 100 | 40820246 | 0.0000123 | 1.12 | 77.78844 | NA | NA | 0.094052 | 0.0022170 | 9024952 | 99.96386 | NA | NA | 93.10 | 38679666 | NA | NA | NA | NA | NA | NA |
| smith | tardbp_3 | 68577024 | 76199035 | 76199035 | 68577024 | 100 | 34276814 | 0.0000219 | 1.11 | 78.46129 | NA | NA | 0.085099 | 0.0020722 | 7622011 | 99.96588 | NA | NA | 93.10 | 32467252 | NA | NA | NA | NA | NA | NA |
| bhinge | iso_1 | 49358770 | 62447827 | 62447827 | 49358770 | 100 | 49358770 | 0.0000268 | 1.06 | NA | NA | NA | 0.455262 | 0.0016714 | 13089057 | 0.00000 | NA | NA | 89.15 | 44074145 | 0.9649444 | NA | 49 | 100.00000 | 15.58140 | 49 |
| bhinge | iso_2 | 57907498 | 75011913 | 75011913 | 57907498 | 100 | 57907498 | 0.0000169 | 1.07 | NA | NA | NA | 0.493924 | 0.0016511 | 17104415 | 0.00000 | NA | NA | 87.86 | 50957825 | 1.0323901 | NA | 50 | 100.00000 | 18.07492 | 50 |
| bhinge | sod1_1 | 57424532 | 74874820 | 74874820 | 57424532 | 100 | 57424532 | 0.0000593 | 1.08 | NA | NA | NA | 0.467025 | 0.0016817 | 17450288 | 0.00000 | NA | NA | 88.12 | 50682994 | 0.9878292 | NA | 50 | 100.00000 | 17.54508 | 50 |
| bhinge | sod1_2 | 46422296 | 59960152 | 59960152 | 46422296 | 100 | 46422296 | 0.0000103 | 1.04 | NA | NA | NA | 0.472328 | 0.0016610 | 13537856 | 0.00000 | NA | NA | 88.05 | 40936487 | 1.0394206 | NA | 50 | 100.00000 | 16.16385 | 50 |
| hawkins | ctrl_1 | 55732128 | 82244817 | 82244817 | 55732128 | 100 | 55732128 | 0.0001172 | 1.04 | NA | NA | NA | 0.402003 | 0.0022973 | 26512689 | 0.00000 | NA | NA | 86.11 | 48794129 | 2.8396430 | NA | 49 | 100.00000 | 36.13990 | 49 |
| hawkins | ctrl_2 | 56249612 | 87079998 | 87079998 | 56249612 | 100 | 56249612 | 0.0001425 | 1.05 | NA | NA | NA | 0.446901 | 0.0022671 | 30830386 | 0.00000 | NA | NA | 84.24 | 48318433 | 3.0143122 | NA | 50 | 100.00000 | 40.06617 | 50 |
| hawkins | fus_1 | 56937877 | 91180287 | 91180287 | 56937877 | 100 | 56937877 | 0.0000613 | 1.05 | NA | NA | NA | 0.434754 | 0.0023454 | 34242410 | 0.00000 | NA | NA | 83.85 | 48671327 | 3.3447031 | NA | 50 | 100.00000 | 39.16021 | 50 |
| hawkins | fus_2 | 55697111 | 91222990 | 91222990 | 55697111 | 100 | 55697111 | 0.0000492 | 1.06 | NA | NA | NA | 0.473655 | 0.0023033 | 35525879 | 0.00000 | NA | NA | 82.82 | 46919285 | 3.2152090 | NA | 51 | 100.00000 | 42.74376 | 50 |
| lee.ALS | spinal_c9orf72_1 | 176059847 | 295475531 | 295475531 | 176059847 | 100 | 176059847 | 0.0000603 | 1.04 | 0.00000 | NA | NA | 0.583518 | 0.0028718 | 119415684 | 0.00000 | NA | NA | 80.38 | 144676081 | 1.3170423 | NA | 48 | 75.49589 | 49.68399 | 48 |
| lee.ALS | spinal_c9orf72_2 | 158118940 | 248292842 | 248292842 | 158118940 | 100 | 158118940 | 0.0000524 | 1.05 | 0.00000 | NA | NA | 0.625328 | 0.0026696 | 90173902 | 0.00000 | NA | NA | 81.79 | 132037661 | 1.5092816 | NA | 48 | 75.49558 | 53.24453 | 48 |
| lee.ALS | spinal_c9orf72_3 | 165519831 | 397216894 | 397216894 | 165519831 | 100 | 165519831 | 0.0000592 | 1.06 | 0.00000 | NA | NA | 0.682174 | 0.0029370 | 231697063 | 0.00000 | NA | NA | 61.79 | 119197894 | 1.3272903 | NA | 51 | 75.49916 | 60.90015 | 51 |
| lee.ALS | spinal_ctrl_1 | 56334539 | 91703261 | 91703261 | 56334539 | 100 | 28153597 | 0.0000924 | 1.04 | 18.87285 | NA | NA | 0.663619 | 0.0039929 | 35368722 | 99.95146 | NA | NA | 79.50 | 23895796 | NA | NA | NA | NA | NA | NA |
| lee.ALS | spinal_ctrl_2 | 67107456 | 106347097 | 106347097 | 67107456 | 100 | 33535748 | 0.0000420 | 1.04 | 17.48065 | NA | NA | 0.696667 | 0.0041699 | 39239641 | 99.94641 | NA | NA | 80.24 | 28822340 | NA | NA | NA | NA | NA | NA |
| lee.ALS | spinal_ctrl_3 | 57737133 | 107257696 | 107257696 | 57737133 | 100 | 28847016 | 0.0004675 | 1.18 | 12.25616 | NA | NA | 0.746278 | 0.0043442 | 49520563 | 99.92535 | NA | NA | 74.28 | 23174968 | NA | NA | NA | NA | NA | NA |
| lee.ALS | spinal_sod1_1 | 130130020 | 224968136 | 224968136 | 130130020 | 100 | 130130020 | 0.0000244 | 1.07 | 0.00000 | NA | NA | 0.590068 | 0.0027903 | 94838116 | 0.00000 | NA | NA | 80.01 | 106453731 | 0.6998293 | NA | 48 | 75.51113 | 50.05608 | 48 |
| lee.ALS | spinal_sod1_2 | 177533609 | 254297645 | 254297645 | 177533609 | 100 | 177533609 | 0.0000394 | 1.06 | 0.00000 | NA | NA | 0.624196 | 0.0026957 | 76764036 | 0.00000 | NA | NA | 84.00 | 151337173 | 1.5103653 | NA | 48 | 75.46761 | 53.56905 | 48 |
| lee.ALS | spinal_sod1_3 | 152556502 | 215300982 | 215300982 | 152556502 | 100 | 152556502 | 0.0000365 | 1.09 | 0.00000 | NA | NA | 0.634475 | 0.0026854 | 62744480 | 0.00000 | NA | NA | 83.98 | 130245147 | 1.7993886 | NA | 48 | 75.49433 | 54.11551 | 48 |
ipsc_mn_als_datasets_with_lee.pcaData <- plotPCA(ipsc_mn_als_datasets_with_lee.vsd, intgroup=c("sample", "dataset", "database_dir", "condition", "mutation", "dataset_sample", "strandedness", "onset_site", "study_accession", "DIV", "instrument","library_type"),
returnData=TRUE) %>% as_tibble() %>%
mutate(dataset = as.character(dataset), dataset = gsub("dafianca","dafinca",dataset), dataset_sample = gsub("dafianca","dafinca",dataset_sample), dataset = case_when(dataset == "neurolincs0" & grepl("^0007",sample) ~ "neurolincs_diMN", dataset == "neurolincsA" & grepl("^A-042",sample) ~ "neurolincs_iMN", dataset == "answerals" ~ "AnswerALS", dataset %in% c("dafinca.c9orf72","dafinca.tardbp") ~ "dafinca", TRUE ~ dataset), library_type = case_when(dataset %in% c("catanese","dafinca","kapeli","kiskinis","luisier","sareen","sommer","smith","sterneckert","wang","lee.CTRL") ~ "poly(A)", TRUE ~ "Total Ribo-Zero"), #dataset = gsub("\\."," ",dataset), #dataset = str_to_title(dataset),
DIV = as.character(DIV), DIV = case_when(is.na(DIV) ~ "30", TRUE ~ DIV), database_dir = gsub("/camp/lab/luscomben/home/shared/projects/patani-collab/public-data","/camp/project/proj-luscombn-patani/working/public-data",database_dir),
) %>%
left_join(select(ipsc_mn_als_datasets_with_lee.metadata, dataset_sample, gender))
# Colour by dataset
ipsc_mn_als_datasets_with_lee.pca_dataset <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, shape = library_type)) + geom_point(aes(color=dataset), size=1) +
scale_color_manual(values = c("AnswerALS"="#94C09B", "neurolincs.iMN"="#A9B7B7", "neurolincs.diMN"="#BEAED4", "bhinge"= "#7FC97F","catanese"="#7FC97F", "dafinca"="#94C09B", "desantis"="#FEEA92", "kapeli"="#A9B7B7", "kiskinis"="#BEAED4", "luisier"="#D3B4BA", "hawkins"="#E8BAA0", "sareen"="#FDC086", "smith"="#FDD58C", "sommer"="#FFFF99", "sterneckert"="#7A9DA8", "wang"="#BCCEA0","lee.CTRL"="#75489F", "lee.ALS"="#386CB0")) +
theme_oz() + theme(legend.text=element_text(size=8), legend.title=element_text(size=7), legend.position = "right", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance")) + #coord_fixed() +
ggforce::geom_mark_ellipse(aes(label = library_type), label.fontsize = 8, label.fontface = "plain", con.type = "straight", con.cap = 0.5, show.legend = FALSE) + guides(color=guide_legend(title="Dataset", keywidth=0.1, keyheight=0.15, default.unit="inch"))
ipsc_mn_als_datasets_with_lee.pca_datasetastrocyte.markers = c("ALDH1L1", "AQP4", "GFAP","EDNRB", "FGFR3", "SLC4A4", "DIO2")
endo.markers = c("CLDN5", "ESAM", "ICAM2", "APOLD1", "NOSTRIN", "ADGRL4", "PECAM1")
myeloid.markers = c("AIF1", "C1QA", "CSF1R", "ITGAM", "PTPRC", "CCL3","IL1A", "TREM2")
oligo.markers = c("MBP", "MOG", "GPR37", "SOX10", "OPALIN", "MOBP", "PLP1")
undifferentiated = c("SOX2","POU5F1","UTF1","REX1","ALPL","TERT","ESRG","CNMD","SFRP2")
neural.precursor = c("NES","SOX1","SOX2","CD133","PAX6","NOTCH1","OCLN","CDH1","CDH2","SOX10","VIM","GFAP")
neural.progenitor = c("MAP2","HUC","HUD","NF","NCAM","DCX","SOX2")
neural.crest <- c("SOX10","NGFR","FOXD3","SNAI1","SNAI2","LMX1A")
dorsal.progenitor <- c("ATOH1","OLIG3","MSX1","PAX3","PAX7","DBX1","DBX2","IRX3","ASCL1")
ho.genes = c("SST","DCX","RFX4","ASCL1","HOXB8","NEFH","SCN1A","TNS1","SPOCK3","SNAP25","TDGF1","POU5F1","L1TD1","FXYD5","PHLDA2","TOP2A","DLGAP5","FZD7","ILF2","MSH2")
nonspecific = c("SOX2")
roof.plate = c("LMX1A","MSX1","MSX2","PAX3","WNT1","GDF7")
dorsal.progenitor = c("IRX3","IRX5","OLIG3","PAX6","ASCL1","GBX2","GSX2","PAX7","GSX1","DBX2","DBX1","SP8")
intermediate.progenitor = c("NKX6-2","PRDM12","FOXN4")
pMN.domain = c("NKX6-1", "OLIG2")
ventral.progenitor = c("NKX2-2","NKX2-8")
floor.plate = c("ARX","FERD3L","FOXA2","LMX1B","SHH")
nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2","ARHGAP36")
V3.domain = c("NKX2-2","SIM1")
nonspecific.neuronal = c("SYT1","MAP2","STMN2","NEFM","SNAP25","SYT4","NCAM1","GAP43","L1CAM","TUBB3","NEFL","ELAVL3")#"NEFH",
motor.neuron.progenitor <- c("OLIG2","NKX6-1","NKX6-2","PAX6","GLI2","FOXA2","NEUROG2","OLIG1","NKX2-2") #"CREBBP","EP300",
postmitotic.motor.neuron <- c("CHAT","MNX1","ISL1","LHX3","FOXP1","ALDH1A2","ETV4","LMO4","ALCAM","SMAD1","ZEB2","SLC18A3")
oculomotor.markers = c("PHOX2A", "PHOX2B", "TBX20", "RGS4","SEMA6D","PLXNA4","EYA2","EYA1","FGF10","EN1")
interneuron.markers <- c(V0.domain,V1,V2a.domain,V2b.domain,V3.domain,"SHOX2")
mn.markers = c(postmitotic.motor.neuron,nonspecific.neuronal)
### Cell type markers
celltype.markers = c(astrocyte.markers, endo.markers, myeloid.markers, oligo.markers, mn.markers)
celltype.markers.df = tibble("gene_name" = celltype.markers) %>% filter(gene_name %in% celltype.markers) %>%
mutate(group = case_when(gene_name %in% astrocyte.markers ~ "astrocyte.markers", gene_name %in% endo.markers ~ "endo.markers",
gene_name %in% myeloid.markers ~ "myeloid.markers", gene_name %in% oligo.markers ~ "oligo.markers",
gene_name %in% mn.markers ~ "mn.markers"),
group = factor(group, levels = c("astrocyte.markers", "endo.markers", "myeloid.markers", "oligo.markers","mn.markers"))) %>%
arrange(group) %>% distinct(gene_name, .keep_all = TRUE)
dataset.samples.df = ipsc_mn_als_datasets_with_lee.metadata %>% select(dataset_sample, dataset) %>% mutate(dataset_sample = gsub("dafinca.tardbp", "dafinca", dataset_sample), dataset_sample = gsub("dafinca.c9orf72", "dafinca", dataset_sample), dataset = gsub("lee.ALS", "lee", dataset), dataset = gsub("lee.CTRL", "lee", dataset), dataset = gsub("mn_d25_", "",dataset), dataset = as.factor(dataset)) %>% filter(!grepl("answerals_CASE",dataset_sample))
# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
celltype.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>%
filter(gene_name %in% celltype.markers.df$gene_name) %>% distinct(gene_name, .keep_all = TRUE) %>%
dplyr::mutate_if(is.numeric, funs((. - min_vst))) %>%
arrange(factor(gene_name, levels = celltype.markers.df$gene_name)) %>% select(-gene_id) %>%
rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>%
select(-contains("answerals_CASE"))
celltype.markers.df.filt = celltype.markers.df %>% filter(gene_name %in% celltype.markers.marker$gene_name)
celltype.markers.marker.mat <- make_matrix(select(celltype.markers.marker,-gene_name), pull(celltype.markers.marker,gene_name))
### Cluster samples ###
celltype.markers.marker.centered_mat = t(scale(t(celltype.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
celltype.markers.marker.scaled_mat = t(scale(t(celltype.markers.marker.mat), center=FALSE,scale=TRUE)) # scaled, not centered
celltype.markers.rnaseq.cluster.heatmap <- Heatmap(t(celltype.markers.marker.mat),
border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"), #, annotation_legend_side = "bottom"), show_heatmap_legend = FALSE,
column_order = celltype.markers.df.filt$gene_name,
column_names_gp = gpar(fontsize = 6),
column_split = celltype.markers.df.filt$group,
bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",5)), labels = c("Astrocyte", "Endothelial", "Myeloid", "Oligodendrocyte","Motor neuron"), labels_gp = gpar(fontsize = 7), labels_rot = 0)), column_title = NULL,
show_row_names = FALSE, #row_names_gp = gpar(fontsize = 6),
# row_order = dataset.samples.df$dataset_sample,
row_split = dataset.samples.df$dataset,
right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)), labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen","Sommer", "Smith", "Sterneckert", "Wang"),
labels_gp = gpar(fontsize = 7), labels_rot = 0)),
row_title = NULL, cluster_rows = FALSE, cluster_column_slices = FALSE, cluster_columns = FALSE)
celltype.markers.rnaseq.cluster.heatmapFig S1 is the PRISMA flow diagram
ipsc_mn_als_datasets_with_lee.vsd.rv <- rowVars(assay(ipsc_mn_als_datasets_with_lee.vsd)) # calculate the variance for each gene
ipsc_mn_als_datasets_with_lee.vsd.ntop_genes <- order(ipsc_mn_als_datasets_with_lee.vsd.rv, decreasing=TRUE)[seq_len(min(500, length(ipsc_mn_als_datasets_with_lee.vsd.rv)))] # select the ntop genes by variance
ipsc_mn_als_datasets_with_lee.vsd.pca <- prcomp(t(assay(ipsc_mn_als_datasets_with_lee.vsd)[ipsc_mn_als_datasets_with_lee.vsd.ntop_genes,])) # perform a PCA on the data in assay(x) for the selected genes
ipsc_mn_als_datasets_with_lee.vsd.loadings <- as_tibble(ipsc_mn_als_datasets_with_lee.vsd.pca$rotation, rownames = "gene_id") %>% left_join(gene2ens) %>% arrange(PC1) %>% select(gene_name, gene_id, everything())
nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2")#,"ARHGAP36")
V3.domain = c("NKX2-2","SIM1")
HOX.markers <- gtf %>% filter(grepl("^HOX[A-D][0-9]+", gene_name)) %>% distinct(gene_name) %>% pull(gene_name)
neuronal.markers = c(nonspecific.neuronal, dl.domains, V0.domain,V1, V2a.domain, V2b.domain,MN.domain,V3.domain)
# scatter all PC1 vs PC2
ipsc_mn_als_datasets_with_lee.vsd.loadings.scatter = ggplot(ipsc_mn_als_datasets_with_lee.vsd.loadings, aes(x = PC1, y = PC2 )) +
labs(x = "PC1 gene loading", y = "PC2 gene loading") +
geom_hline(yintercept = 0, linetype = 3) + geom_vline(xintercept = 0, linetype = 3) +
geom_point(size = 1, alpha = 0.1) +
scale_fill_continuous(type = "viridis") +
guides(fill = FALSE) +
theme_oz() +
geom_text_repel(data = filter(ipsc_mn_als_datasets_with_lee.vsd.loadings, abs(PC1) > 0.04, abs(PC2) > 0.04, grepl("^H[1-9]",gene_name)), aes(x = PC1, y = PC2, label = gene_name), colour = "firebrick2", size = 2.3) +
geom_text_repel(data = filter(ipsc_mn_als_datasets_with_lee.vsd.loadings, abs(PC1) > 0.04, abs(PC2) > 0.04, grepl("^SNOR|RN7SK|RMRP|RPPH1",gene_name)), aes(x = PC1, y = PC2, label = gene_name), colour = "firebrick2", size = 2.3) +
geom_text_repel(data = filter(ipsc_mn_als_datasets_with_lee.vsd.loadings, gene_name %in% c(neuronal.markers, HOX.markers)), aes(x = PC1, y = PC2, label = gene_name), colour = "black", size = 2.3) +
annotate("text", x = 0.04, y = 0.05, label = "PC1+ PC2+",size = 3, color = "black") + annotate("text", x = -0.07, y = -0.12, label = "PC1- PC2-", size = 3, color = "firebrick2") +
annotate("text", x = 0.04, y = -0.12, label = "PC1+ PC2-", size = 3, color = "black") + annotate("text", x = -0.07, y = 0.05, label = "PC1- PC2+", size = 3, color = "black")
ipsc_mn_als_datasets_with_lee.vsd.loadings.scatteripsc_mn_als_datasets_with_lee.pcaData <- plotPCA(ipsc_mn_als_datasets_with_lee.vsd, intgroup=c("sample", "dataset", "database_dir", "condition", "mutation", "dataset_sample", "strandedness", "onset_site", "study_accession", "DIV", "instrument","library_type"),
returnData=TRUE) %>% as_tibble() %>%
mutate(dataset = as.character(dataset), dataset = gsub("dafianca","dafinca",dataset), dataset_sample = gsub("dafianca","dafinca",dataset_sample), dataset = case_when(dataset == "neurolincs0" & grepl("^0007",sample) ~ "neurolincs_diMN", dataset == "neurolincsA" & grepl("^A-042",sample) ~ "neurolincs_iMN", dataset == "answerals" ~ "AnswerALS", dataset %in% c("dafinca.c9orf72","dafinca.tardbp") ~ "dafinca", TRUE ~ dataset),
DIV = as.character(DIV), DIV = case_when(is.na(DIV) ~ "30", TRUE ~ DIV), database_dir = gsub("/camp/lab/luscomben/home/shared/projects/patani-collab/public-data","/camp/project/proj-luscombn-patani/working/public-data",database_dir),
library_type = case_when(dataset %in% c("catanese","dafinca","kapeli","kiskinis","luisier","mitchell","sareen","sommer","smith","sterneckert","wang","lee.CTRL") ~ "poly(A)", TRUE ~ "Total Ribo-Zero")) %>%
left_join(select(ipsc_mn_als_datasets_with_lee.metadata, dataset_sample, gender))
# multiqc stats
multiqc_general_stats_stat_paths = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir) %>% mutate(multiqc_general_stats_stat_paths = paste0(database_dir,"/nfcore/multiqc/star_salmon/multiqc_data/multiqc_general_stats.txt"),
# multiqc_general_stats_stat_paths = gsub("/camp/lab/luscomben/home/users/ziffo|/camp/project","/Volumes/lab-luscomben/home/users/ziffo",multiqc_general_stats_stat_paths)
) %>% pull(multiqc_general_stats_stat_paths)
multiqc_general_stats.tsv = multiqc_general_stats_stat_paths %>% map(read_tsv, show_col_types = FALSE)
names(multiqc_general_stats.tsv) = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir,.keep_all=TRUE) %>% pull(database_dir)
multiqc_general_stats <- map_dfr(multiqc_general_stats.tsv, bind_rows, .id = "database_dir") %>% clean_names()
multiqc_rseqc_read_distribution_paths = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir) %>% mutate(multiqc_rseqc_read_distribution_paths = paste0(database_dir,"/nfcore/multiqc/star_salmon/multiqc_data/multiqc_rseqc_read_distribution.txt"),
# multiqc_rseqc_read_distribution_paths = gsub("/camp/lab/luscomben/home/users/ziffo|/camp/project","/Volumes/lab-luscomben/home/users/ziffo",multiqc_rseqc_read_distribution_paths)
) %>% pull(multiqc_rseqc_read_distribution_paths)
multiqc_rseqc_read_distribution.tsv = multiqc_rseqc_read_distribution_paths %>% map(read_tsv, show_col_types = FALSE)
names(multiqc_rseqc_read_distribution.tsv) = ipsc_mn_als_datasets_with_lee.metadata %>% distinct(database_dir,.keep_all=TRUE) %>% pull(database_dir)
multiqc_rseqc_read_distribution <- map_dfr(multiqc_rseqc_read_distribution.tsv, bind_rows, .id = "database_dir") %>% clean_names()
ipsc_mn_als_datasets_with_lee.pcaData = ipsc_mn_als_datasets_with_lee.pcaData %>% left_join(multiqc_general_stats) %>% left_join(multiqc_rseqc_read_distribution) # need unique sample names - If multiple dataset names within a single multiqc_general_stats.txt then will only join the first dataset name
# Colour by dataset
ipsc_mn_als_datasets_with_lee.pca_dataset <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=dataset)) + geom_point(size=1) +
scale_color_manual(values = c("AnswerALS"="#94C09B", "neurolincs.iMN"="#A9B7B7", "neurolincs.diMN"="#BEAED4", "bhinge"= "#7FC97F","catanese"="#7FC97F", "dafinca"="#94C09B", "desantis"="#FEEA92", "kapeli"="#A9B7B7", "kiskinis"="#BEAED4", "luisier"="#D3B4BA", "hawkins"="#E8BAA0", "sareen"="#FDC086", "smith"="#FDD58C", "sommer"="#FFFF99", "sterneckert"="#7A9DA8", "wang"="#BCCEA0","lee.CTRL"="#75489F", "lee.ALS"="#386CB0")) +
theme_oz() + theme(legend.position = "none") + guides(color=guide_legend(keywidth=0.5, keyheight=0.5, default.unit="inch")) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance")) + #coord_fixed() +
ggforce::geom_mark_ellipse(aes(label = dataset), label.fontsize = 8, label.fontface = "plain", con.type = "straight", con.cap = 0.5, show.legend = FALSE)
ipsc_mn_als_datasets_with_lee.pca_dataset# Colour by library_type
ipsc_mn_als_datasets_with_lee.pca_library_type <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=library_type)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))+labs(colour="Library preparation")
ipsc_mn_als_datasets_with_lee.pca_library_type# Colour by instrument
ipsc_mn_als_datasets_with_lee.pca_instrument <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=instrument)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_blank(), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_instrument# Colour by DIV
ipsc_mn_als_datasets_with_lee.pca_DIV <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=DIV)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch", title.position = "top")) + labs(color="Days in vitro") +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_DIV# Colour by ALS
ipsc_mn_als_datasets_with_lee.pca_als <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=condition)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch", title.position = "top")) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_als# Colour by mutation
ipsc_mn_als_datasets_with_lee.pca_mutation <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=mutation)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_mutation# Colour by gender
ipsc_mn_als_datasets_with_lee.pca_gender <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=gender)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.1, keyheight=0.1, default.unit="inch")) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_genderFig S3
# Colour by strandedness
ipsc_mn_als_datasets_with_lee.pca_strandedness <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=strandedness)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=7), legend.position = "top", legend.spacing = unit(0.01, 'cm')) + guides(color=guide_legend(keywidth=0.2, keyheight=0.2, default.unit="inch")) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_strandedness# Colour by read depth
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_raw_total_sequences <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=samtools_mqc_generalstats_samtools_raw_total_sequences)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6, angle = 0), legend.title=element_text(size=7), legend.position = "top", legend.box = "vertical", legend.spacing = unit(1, 'cm')) +
guides(color = guide_colourbar(title = "read depth", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top")) +
scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$samtools_mqc_generalstats_samtools_raw_total_sequences,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_raw_total_sequences# Color by intronic read % intron_read_pct
ipsc_mn_als_datasets_with_lee.pca_read_distribution <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=introns_tag_pct)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) +
guides(color = guide_colourbar(title = "intronic reads %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top")) +
scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$introns_tag_pct,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_read_distribution# Colour by biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna
ipsc_mn_als_datasets_with_lee.pca_biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) +
guides(color = guide_colourbar(title = "ribosomal rna %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top")) +
scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_biotype_counts_mqc_generalstats_biotype_counts_percent_r_rna# Colour by quali_map_mqc_generalstats_qualimap_5_3_bias
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_5_3_bias <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=quali_map_mqc_generalstats_qualimap_5_3_bias)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) +
guides(color = guide_colourbar(title = "5' 3' bias", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top")) +
scale_color_gradient2(midpoint=1, low="blue", mid="white", high="red", label=comma) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_5_3_bias# Colour by quali_map_mqc_generalstats_qualimap_reads_aligned
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_reads_aligned <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=quali_map_mqc_generalstats_qualimap_reads_aligned)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) +
guides(color = guide_colourbar(title = "Reads aligned", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top")) +
scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$quali_map_mqc_generalstats_qualimap_reads_aligned,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_quali_map_mqc_generalstats_qualimap_reads_aligned# Colour by picard_mqc_generalstats_picard_percent_duplication
ipsc_mn_als_datasets_with_lee.pca_picard_mqc_generalstats_picard_percent_duplication <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=picard_mqc_generalstats_picard_percent_duplication)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) +
guides(color = guide_colourbar(title = "Read duplication %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top")) +
scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$picard_mqc_generalstats_picard_percent_duplication,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_picard_mqc_generalstats_picard_percent_duplication# Colour by samtools_mqc_generalstats_samtools_reads_mapped
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_reads_mapped <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=samtools_mqc_generalstats_samtools_reads_mapped)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) +
guides(color = guide_colourbar(title = "Reads mapped", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top")) +
scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$samtools_mqc_generalstats_samtools_reads_mapped,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_samtools_mqc_generalstats_samtools_reads_mapped# Colour by star_mqc_generalstats_star_uniquely_mapped_percent
ipsc_mn_als_datasets_with_lee.pca_star_mqc_generalstats_star_uniquely_mapped_percent <- ggplot(ipsc_mn_als_datasets_with_lee.pcaData, aes(PC1, PC2, color=star_mqc_generalstats_star_uniquely_mapped_percent)) + geom_point(size=1) +
theme_oz() + theme(legend.text=element_text(size=6), legend.title=element_text(size=6), legend.position = "top", legend.box = "vertical", legend.spacing = unit(0.1, 'cm')) +
guides(color = guide_colourbar(title = "Reads uniquely mapped %", barwidth = 15, barheight = 0.5, ticks = FALSE, title.position = "top")) +
scale_color_gradient2(midpoint=mean(ipsc_mn_als_datasets_with_lee.pcaData$star_mqc_generalstats_star_uniquely_mapped_percent,na.rm=TRUE), low="blue", mid="white", high="red", label=comma) +
xlab(paste0("PC1: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[1],"% variance")) + ylab(paste0("PC2: ",round(100 * attr(ipsc_mn_als_datasets_with_lee.pcaData, "percentVar"))[2],"% variance"))
ipsc_mn_als_datasets_with_lee.pca_star_mqc_generalstats_star_uniquely_mapped_percentastrocyte.markers = c("ALDH1L1", "AQP4", "GFAP","EDNRB", "FGFR3", "SLC4A4", "DIO2")
endo.markers = c("CLDN5", "ESAM", "ICAM2", "APOLD1", "NOSTRIN", "ADGRL4", "PECAM1")
myeloid.markers = c("AIF1", "C1QA", "CSF1R", "ITGAM", "PTPRC", "CCL3","IL1A", "TREM2")
oligo.markers = c("MBP", "MOG", "GPR37", "SOX10", "OPALIN", "MOBP", "PLP1")
undifferentiated = c("SOX2","POU5F1","UTF1","REX1","ALPL","TERT","ESRG","CNMD","SFRP2")
neural.precursor = c("NES","SOX1","SOX2","CD133","PAX6","NOTCH1","OCLN","CDH1","CDH2","SOX10","VIM","GFAP")
neural.progenitor = c("MAP2","HUC","HUD","NF","NCAM","DCX","SOX2")
neural.crest <- c("SOX10","NGFR","FOXD3","SNAI1","SNAI2","LMX1A")
dorsal.progenitor <- c("ATOH1","OLIG3","MSX1","PAX3","PAX7","DBX1","DBX2","IRX3","ASCL1")
ho.genes = c("SST","DCX","RFX4","ASCL1","HOXB8","NEFH","SCN1A","TNS1","SPOCK3","SNAP25","TDGF1","POU5F1","L1TD1","FXYD5","PHLDA2","TOP2A","DLGAP5","FZD7","ILF2","MSH2")
nonspecific = c("SOX2")
roof.plate = c("LMX1A","MSX1","MSX2","PAX3","WNT1","GDF7")
dorsal.progenitor = c("IRX3","IRX5","OLIG3","PAX6","ASCL1","GBX2","GSX2","PAX7","GSX1","DBX2","DBX1","SP8")
intermediate.progenitor = c("NKX6-2","PRDM12","FOXN4")
pMN.domain = c("NKX6-1", "OLIG2")
ventral.progenitor = c("NKX2-2","NKX2-8")
floor.plate = c("ARX","FERD3L","FOXA2","LMX1B","SHH")
nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2","ARHGAP36")
V3.domain = c("NKX2-2","SIM1")
nonspecific.neuronal = c("SYT1","MAP2","STMN2","NEFM","SNAP25","SYT4","NCAM1","GAP43","L1CAM","TUBB3","NEFL","ELAVL3")
motor.neuron.progenitor <- c("OLIG2","NKX6-1","NKX6-2","PAX6","GLI2","FOXA2","NEUROG2","OLIG1","NKX2-2")
postmitotic.motor.neuron <- c("CHAT","MNX1","ISL1","LHX3","FOXP1","ALDH1A2","ETV4","LMO4","ALCAM","SMAD1","ZEB2","SLC18A3")
oculomotor.markers = c("PHOX2A", "PHOX2B", "TBX20", "RGS4","SEMA6D","PLXNA4","EYA2","EYA1","FGF10","EN1")
interneuron.markers <- c(V0.domain,V1,V2a.domain,V2b.domain,V3.domain,"SHOX2")
mn.markers = c(postmitotic.motor.neuron,nonspecific.neuronal)
### Cell type markers
celltype.markers = c(astrocyte.markers, endo.markers, myeloid.markers, oligo.markers, mn.markers)
celltype.markers.df = tibble("gene_name" = celltype.markers) %>% filter(gene_name %in% celltype.markers) %>%
mutate(group = case_when(gene_name %in% astrocyte.markers ~ "astrocyte.markers", gene_name %in% endo.markers ~ "endo.markers",
gene_name %in% myeloid.markers ~ "myeloid.markers", gene_name %in% oligo.markers ~ "oligo.markers",
gene_name %in% mn.markers ~ "mn.markers"),
group = factor(group, levels = c("astrocyte.markers", "endo.markers", "myeloid.markers", "oligo.markers","mn.markers"))) %>%
arrange(group) %>% distinct(gene_name, .keep_all = TRUE)
dataset.samples.df = ipsc_mn_als_datasets_with_lee.metadata %>% select(dataset_sample, dataset) %>% mutate(dataset_sample = gsub("dafinca.tardbp", "dafinca", dataset_sample), dataset_sample = gsub("dafinca.c9orf72", "dafinca", dataset_sample), dataset = gsub("lee.ALS", "lee", dataset), dataset = gsub("lee.CTRL", "lee", dataset), dataset = gsub("mn_d25_", "",dataset), dataset = as.factor(dataset)) %>% filter(!grepl("answerals_CASE",dataset_sample))
# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
celltype.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>%
filter(gene_name %in% celltype.markers.df$gene_name) %>% distinct(gene_name, .keep_all = TRUE) %>%
dplyr::mutate_if(is.numeric, funs((. - min_vst))) %>%
arrange(factor(gene_name, levels = celltype.markers.df$gene_name)) %>% select(-gene_id) %>%
rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>%
select(-contains("answerals_CASE"))
celltype.markers.df.filt = celltype.markers.df %>% filter(gene_name %in% celltype.markers.marker$gene_name)
celltype.markers.marker.mat <- make_matrix(select(celltype.markers.marker,-gene_name), pull(celltype.markers.marker,gene_name))
### Cluster samples ###
celltype.markers.marker.centered_mat = t(scale(t(celltype.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
celltype.markers.marker.scaled_mat = t(scale(t(celltype.markers.marker.mat), center=FALSE,scale=TRUE)) # scaled, not centered
celltype.markers.rnaseq.cluster.heatmap <- Heatmap(t(celltype.markers.marker.mat),
border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"), #, annotation_legend_side = "bottom"), show_heatmap_legend = FALSE,
column_order = celltype.markers.df.filt$gene_name,
column_names_gp = gpar(fontsize = 6),
column_split = celltype.markers.df.filt$group,
bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",5)), labels = c("Astrocyte", "Endothelial", "Myeloid", "Oligodendrocyte","Motor neuron"), labels_gp = gpar(fontsize = 7), labels_rot = 0)), column_title = NULL,
show_row_names = FALSE, #row_names_gp = gpar(fontsize = 6),
# row_order = dataset.samples.df$dataset_sample,
row_split = dataset.samples.df$dataset,
right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)), labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen","Sommer", "Smith", "Sterneckert", "Wang"),
labels_gp = gpar(fontsize = 7), labels_rot = 0)),
row_title = NULL, cluster_rows = FALSE, cluster_column_slices = FALSE, cluster_columns = FALSE)
celltype.markers.rnaseq.cluster.heatmapnonspecific.neuronal = c("SYT1","MAP2","STMN2","NEFM","SNAP25","SYT4","NCAM1","GAP43","L1CAM","TUBB3","NEFL","ELAVL3")#,"NEFH"
motor.neuron.progenitor <- c("OLIG2","NKX6-1","NKX6-2","PAX6","GLI2","FOXA2","NEUROG2","OLIG1","NKX2-2") #"CREBBP","EP300",
postmitotic.motor.neuron <- c("CHAT","MNX1","ISL1","LHX3","FOXP1","ALDH1A2","ETV4","LMO4","ALCAM","SMAD1","ZEB2","SLC18A3","ETV1", "NOS1","RUNX1","NOTCH1","ARHGAP36","SLC10A4","POU3F1","FOXP2","ISL2") #
oculomotor.markers = c("PHOX2A", "PHOX2B", "TBX20", "RGS4","SEMA6D","PLXNA4","EYA2","EYA1","FGF10","EN1")
interneuron.markers <- c(V0.domain,V1,V2a.domain,V2b.domain,V3.domain,"SHOX2")#dl.domains LDB1 "LHX1","POU4F1",,"LBX1""LHX2","LHX9","DRGX","LMX1B","VSX2","EVX2","LMO4"
mn.markers = c(postmitotic.motor.neuron,nonspecific.neuronal)
neuron.type.markers = c(motor.neuron.progenitor, postmitotic.motor.neuron, nonspecific.neuronal,interneuron.markers)
neuron.type.markers.df = tibble("gene_name" = neuron.type.markers) %>% filter(gene_name %in% neuron.type.markers) %>%
mutate(group = case_when(gene_name %in% nonspecific.neuronal ~ "nonspecific.neuronal", gene_name %in% motor.neuron.progenitor ~ "motor.neuron.progenitor",
gene_name %in% postmitotic.motor.neuron ~ "postmitotic.motor.neuron", #gene_name %in% oculomotor.markers ~ "oculomotor.markers",
gene_name %in% interneuron.markers ~ "interneuron"),
group = factor(group, levels = c("nonspecific.neuronal", "motor.neuron.progenitor", "postmitotic.motor.neuron", "interneuron"))) %>%
arrange(group) %>% distinct(gene_name, .keep_all = TRUE)
dataset.samples.df = ipsc_mn_als_datasets_with_lee.metadata %>% select(dataset_sample, dataset) %>% mutate(dataset_sample = gsub("dafinca.tardbp", "dafinca", dataset_sample), dataset_sample = gsub("dafinca.c9orf72", "dafinca", dataset_sample), dataset = gsub("lee.ALS", "lee", dataset), dataset = gsub("lee.CTRL", "lee", dataset), dataset = gsub("mn_d25_", "",dataset), dataset = as.factor(dataset)) %>% filter(!grepl("answerals_CASE",dataset_sample))
# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
neuron.type.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>%
filter(gene_name %in% neuron.type.markers.df$gene_name) %>% distinct(gene_name, .keep_all = TRUE) %>%
dplyr::mutate_if(is.numeric, funs((. - min_vst))) %>%
arrange(factor(gene_name, levels = neuron.type.markers.df$gene_name)) %>% select(-gene_id) %>%
rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>%
select(-contains("answerals_CASE"))
neuron.type.markers.df.filt = neuron.type.markers.df %>% filter(gene_name %in% neuron.type.markers.marker$gene_name)
neuron.type.markers.marker.mat <- make_matrix(select(neuron.type.markers.marker,-gene_name), pull(neuron.type.markers.marker,gene_name))
### Cluster samples ###
neuron.type.markers.rnaseq.heatmap <- Heatmap(t(neuron.type.markers.marker.mat),
border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"), #, annotation_legend_side = "bottom"), show_heatmap_legend = FALSE,
column_order = neuron.type.markers.df.filt$gene_name,
column_names_gp = gpar(fontsize = 6),
column_split = factor(neuron.type.markers.df.filt$group, levels = c("nonspecific.neuronal", "motor.neuron.progenitor", "postmitotic.motor.neuron", "interneuron")),
bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",4)), labels = c("nonspecific\nneuronal", "motor neuron\nprogenitor", "postmitotic\nmotor neuron", "interneuron"), labels_gp = gpar(fontsize = 7), labels_rot = 0)),
column_title = NULL,
show_row_names = FALSE,
# row_order = dataset.samples.df$dataset_sample,
row_split = dataset.samples.df$dataset,
right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)),
labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen","Sommer", "Smith", "Sterneckert", "Wang"),
labels_gp = gpar(fontsize = 7), labels_rot = 0)),
row_title = NULL, cluster_rows = FALSE, cluster_column_slices = FALSE, cluster_columns = FALSE)
neuron.type.markers.rnaseq.heatmapMarkers are from Fig 2 in https://journals.biologists.com/dev/article/148/15/dev199711/271192/Single-cell-transcriptome-profiling-of-the-human
nonspecific.neuronal = c("ELAVL3","MAP2","STMN2")
dl1.domain = c("BARHL1","BARHL2","LHX2","LHX9","ATOH1")
dl2.domain = c("FOXD3","LHX5")
dl3.domain = c("POU4F1","OTP","TLX3")
dl4.domain = c("LHX1","PAX8","LBX1","PAX2","GBX1","PTF1A")
dl5.domain = c("GSX1","GSX2","PAX3","PAX7","LMX1B","ASCL1")
dl6.domain = c("DMRT3","WT1")
dl.domains = c(dl1.domain,dl2.domain,dl3.domain,dl4.domain,dl5.domain,dl6.domain)
V0.domain = c("EVX1","EVX2","PITX2")
V1 = c("EN1")
V2a.domain = c("LHX3","SOX14","SOX21","VSX2","FOXN4","VSX1")
V2b.domain = c("GATA2","GATA3","TAL1","MSX1")
MN.domain = c("ISL1","ISL2","MNX1","SLC10A4","SLC18A3","OLIG2","ALDH1A2","ARHGAP36")
V3.domain = c("NKX2-2","SIM1")
neuronal.markers = c(dl.domains, V0.domain,V1, V2a.domain, V2b.domain,MN.domain,V3.domain) #nonspecific.neuronal
neuronal.markers.df = tibble("gene_name" = neuronal.markers) %>%
mutate(group = case_when(gene_name %in% nonspecific.neuronal ~ "nonspecific.neuronal", gene_name %in% dl.domains ~ "dl.domains",
gene_name %in% V0.domain ~ "V0.domain", gene_name %in% V1 ~ "V1",
gene_name %in% V2a.domain ~ "V2a.domain", gene_name %in% V2b.domain ~ "V2b.domain", gene_name %in% MN.domain ~ "MN.domain", gene_name %in% V3.domain ~ "V3.domain"),
group = factor(group, levels = c("dl.domains","V0.domain", "V1", "V2a.domain", "V2b.domain", "MN.domain", "V3.domain"))) %>%
arrange(group) %>% distinct(gene_name, .keep_all = TRUE)
# together with other datasets
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
neuronal.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>%
filter(gene_name %in% neuronal.markers.df$gene_name) %>%
dplyr::mutate_if(is.numeric, funs((. - min_vst))) %>%
arrange(factor(gene_name, levels = neuronal.markers.df$gene_name)) %>% select(-gene_id) %>%
rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>% select(-contains("answerals_CASE"))
neuronal.markers.marker.mat <- make_matrix(select(neuronal.markers.marker,-gene_name), pull(neuronal.markers.marker,gene_name))
### Cluster samples ###
neuronal.markers.marker.centered_mat = t(scale(t(neuronal.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
dorsoventral.markers.heatmap <- Heatmap(t(neuronal.markers.marker.mat),
border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"),
column_order = neuronal.markers.df$gene_name,
column_names_gp = gpar(fontsize = 7),
column_split = neuronal.markers.df$group,
bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",7)), labels = c("dl\ndomains","V0\ndomain", "V1", "V2a\ndomain", "V2b\ndomain", "MN\ndomain", "V3"), labels_gp = gpar(fontsize = 7), labels_rot = 0)),
column_title = NULL, column_title_gp = gpar(fontsize = 8),
cluster_columns = FALSE, cluster_column_slices = FALSE,
cluster_rows = FALSE,
row_title = NULL,
row_split = dataset.samples.df$dataset,
show_row_names = FALSE,
right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",18)),
labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen", "Sommer", "Smith", "Sterneckert", "Wang"),
labels_gp = gpar(fontsize = 7), labels_rot = 0)))
dorsoventral.markers.heatmapHOX markers
HOX.markers <- gtf %>% filter(grepl("^HOX[A-D][0-9]+", gene_name)) %>% distinct(gene_name) %>% pull(gene_name)
HOX.markers.df <- data.frame(row.names = HOX.markers, gene_name = HOX.markers) %>%
mutate(group = gsub("HOX[A-D]","", gene_name), group = factor(as.numeric(gsub("-AS$","", group)))) %>%
arrange(group) %>%
mutate(level = factor(case_when(group %in% c(1,2,3) ~ "Hindbrain", group %in% c(4,5,6,7) ~ "Cervical", group %in% c(8,9) ~ "Thoracic",
group %in% c(10,11) ~ "Lumbar", TRUE ~ "Sacral"), levels = c("Hindbrain","Cervical","Thoracic","Lumbar","Sacral")))
min_vst = min(ipsc_mn_als_datasets_with_lee.vsd.counts[,2])
HOX.markers.marker <- ipsc_mn_als_datasets_with_lee.vsd.counts %>% distinct(gene_name, .keep_all = TRUE) %>%
filter(gene_name %in% HOX.markers.df$gene_name) %>%
dplyr::mutate_if(is.numeric, funs((. - min_vst))) %>%
arrange(factor(gene_name, levels = HOX.markers.df$gene_name)) %>% select(-gene_id) %>%
rename_with(~ gsub("mn_d25_", "", .x, fixed = TRUE)) %>%
select(-contains("answerals_CASE"))
HOX.markers.marker.mat <- make_matrix(select(HOX.markers.marker,-gene_name), pull(HOX.markers.marker,gene_name))
HOX.markers.marker.centered.mat = t(scale(t(HOX.markers.marker.mat), center=TRUE,scale=FALSE)) # centered, not scaled
HOX.markers.heatmap <- Heatmap(t(HOX.markers.marker.mat),
border = TRUE, heatmap_legend_param = list(title = "", direction = "vertical"),
column_order = HOX.markers.df$gene_name,
column_names_gp = gpar(fontsize = 7),
column_split = HOX.markers.df$level,
bottom_annotation = columnAnnotation(markers = anno_block(gp = gpar(fill = rep("white",5)), labels = c("Hindbrain", "Cervical", "Thoracic","Lumbar","Sacral"), labels_gp = gpar(fontsize = 8), labels_rot = 0)),
column_title = NULL, column_title_gp = gpar(fontsize = 8),
cluster_columns = FALSE, cluster_column_slices = FALSE,
cluster_rows = FALSE,
row_title = NULL,
# row_order = dataset.samples.df$dataset_sample,
row_split = dataset.samples.df$dataset,
show_row_names = FALSE,
right_annotation = rowAnnotation(datasets = anno_block(gp = gpar(fill = rep("white",17)),
labels = c("AnswerALS", "Bhinge", "Catanese", "Dafinca\nC9orf72", "Dafinca\nTARDBP", "De Santis", "Hawkins", "Kapeli", "Kiskinis", "Lee", "Luisier", "NeuroLINCS\ndiMN batch", "NeuroLINCS\niMN batch", "Sareen", "Sommer", "Smith", "Sterneckert", "Wang"),
labels_gp = gpar(fontsize = 7), labels_rot = 0)))
HOX.markers.heatmap